yarden / miso Goto Github PK

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

Home Page: http://genes.mit.edu/burgelab/miso/index.html

Shell 0.29% Python 24.80% C 74.19% Batchfile 0.03% C++ 0.10% WebAssembly 0.16% Makefile 0.02% Lex 0.09% sed 0.04% R 0.26% Fortran 0.01%

miso's People

Contributors

Stargazers

Watchers

miso's Issues

Problem with assigned_counts

In the method "count_isoform_assignments" in the file "reads_utils.py" if one of the transcripts has not been assigned a read then it is never returned with 0 value and eventually is missed in the output column "assigned_counts".

eg consider a gene with 4 transcripts of which only the first 2 are assigned reads. In this case transcirpts 3 and 4 are never returned by the method.

Run MCMC until convergence, instead of a fixed number of steps

BAM reader mixes up the TLEN field

This happens if you only read a region, for paired-end reads, obviously. It seems that it is a samtools bug.

Sashimi plot Error: need --output-dir

I tried to run sashimi plot in 2 Ubuntu systems, both comes with Python 2.6.5.

When I execute sashimi plot by python python plot.py --plot-insert-len xxx.insert_len --output-dir plots/

it ways halts with "Error: need --output-dir"

I checked on the source code a bit.

if options.output_dir == None:
    print "Error: need --output-dir"
    sys.exit(1)

It seems like .output_dir is not correctly parsed by OptionParser.

I have installed matplotlib, pysam and scipy in both systems.

Fix up RPKM labels and align Psi tracks

Fix up RPKM labels and give better vertical alignment of Psi tracks.

Detecting low or unrepresented transcripts

I have run Miso (great manual), but it is not pulling out my gene (2 Exons knocked out)

What settings do I need to include transcripts with low to no reads compared to the control?

I'm trying filter_results = False min_event_reads = 0 at the moment.

Thanks alig

Difficulty with malloc error

Hi,

I'm running Miso on Mac OS X 10.8.3 and am having frequent errors of this sort:

Python(57341) malloc: *** error for object 0x104120d00: incorrect checksum for freed object - object was probably modified after being freed.

I am running the --compute-genes-from-file step and looking at alternative splicing events.

Thanks

Test Python RNG in the C code.

Use fragment length correctly in the C solver.

Eliminate delta posteriors output

Creates excessive number of files currently. If there is user interest, willing to implement an sqlite database that stores the delta posteriors - this will dramatically reduce the number of files and the footprint, will be universally accessible, etc.

Order the GFF file, don't assume it was ordered, in the C code.

Reorganize GFF annotations, add new ones

Add sanitized GFF annotations for events. Also offer annotations with introns. Reorganize annotations into systematic categories on separate page in manual and link to it. Clearly separate exon-centric and isoform-centric annotations.

Eliminate all scipy code from code base

scipy still too difficult for most users to install. Replace all KDE-related code and other statistical code that uses scipy.stats with numpy-based alternative.

Convert all parsing from GFF3 to GTF

GFF3 causes major issues. Switch to GTF format, while keeping GFF3 support (internally convert to GTF).

Add note on how to install python packages

Guidelines on Python packages installation

Better CIGAR string support

Right now only M and N tags are recognized, and behavior is undefined for others.

BAM versus GFF header diagnostic tool

Script to check that the BAM headers (chromosome names) and the GFF headers match, i.e. that UCSC genome mapped reads are not being run on Ensembl derived events, or vice versa, to help users debug.

Add option that disables parent jobs from waiting on children jobs

Re: request from UNC users.

Check for presence of BAM index

Check for presence of BAM index (.bai) in the same directory as the BAM.

Update documentation for using `miso` instead of `run_events_analysis.py` and friends

Hello,
When I attempt to use run_events_analysis.py, I get the error:

MISO (Mixture of Isoforms model)
run_events_analysis.py interface is deprecated. Please run 'miso' instead.

But there are no examples or documentation on http://genes.mit.edu/burgelab/miso/docs/. Please add some instructions on how to run standalone miso.

Thanks,
Olga

Variable read length

Within a single data set. This seems to be needed for working with Trinity output files.

Fix `miso_zip.py` for Ensembl style chromosomes

"""
miso_zip.py does not work for Ensembl style chromosome titles. I think this is because sql tables cannot have integer names hence
CREATE TABLE 11 (...)
fails.

I added an incredibly naive patch that appends chr to the chromosome name if it doesn't already start with 'chr', though I'm sure something more extensible exists.

Cheers,

Isaac
"""

Create compressed output for MISO

Potentially use zlib or arcode. At best a ~3 fold reduction in total file size. Consider concatenating multiple event files from same batch.

Fix Python version path issue

Fix Python version path issue. Automatically retrieve correct Python path within run_events_analysis.

misopy not finding paired mates from Tophat Bam

Hi,

I'm trying to compute the insert length distribution given a constitutive exons file.
The bam file comes from TopHat, but misopy is complaining that there are no read pairs, though Flagstat claims otherwise. I tried --no-bam-filter but it made no difference.
I have checked the fastq files & the pairs have the same IDs except of course 1 for R1 & 2 for R2.

Any help would be greatly appreciated. This is my command & error output. Thanks ali

python misopy/pe_utils.py --no-bam-filter --compute-insert-len tophat2.mm10.bam misopy-0.4.6/exons/Mus_musculus.NCBIM37.65.min_1000.const_exons.gff --output-dir /misopy-0.4.6/insert-dist/
Computing insert length distribution of 1 files:
tophat2.mm10.bam

Using const. exons from: misopy-0.4.6/exons/Mus_musculus.NCBIM37.65.min_1000.const_exons.gff
Outputting to: misopy-0.4.6/insert-dist
Minimum exon size used: 500
Getting constitutive exons...
Input GFF: misopy-0.4.6/exons/Mus_musculus.NCBIM37.65.min_1000.const_exons.gff
Output dir: misopy-0.4.6/insert-dist
Output format: gff
Including only exons greater than or equal to 500-bp
Constitutive exons GFF was given, so not outputting another one.
Turning off filtering of BAM reads
Fetching reads in constitutive exons
Mapping BAM to GFF...
BAM: tophat2.mm10.bam
GFF: misopy-0.4.6/exons/Mus_musculus.NCBIM37.65.min_1000.const_exons.gff
Output file: misopy-0.4.6/insert-dist/bam2gff_Mus_musculus.NCBIM37.65.min_1000.const_exons.gff/tophat2.mm10.bam
WARNING: misopy-0.4.6/insert-dist/bam2gff_Mus_musculus.NCBIM37.65.min_1000.const_exons.gff/tophat2.mm10.bam exists. Skipping..
Filtered out 0 read pairs that were on same strand.
Filtered out 0 reads that had no paired mate.
Total read pairs: 0
WARNING: no paired mates in tophat2.mm10.bam. Skipping...
Are you sure the read IDs match? If your BAM paired flags are unset, try using --no-bam-filter

Convert GFF to Python object.

And back. Use the functions in GFF.py.

Can Miso compare more than one mutant with a Wild type

Hi,

Can Miso compare more than one WT/control to more than one Mutant/knockdown?

This would be really useful

Thanks alig

Make MISO output a list of job IDs when using "--use-cluster"

Make MISO output a list of job IDs when used on the cluster. Make a companion script that checks if all the jobs have finished.

Filtering function

Filtering out reads that

don't have a mate, paired end,
incorrect strands for paired end.

Sanitize and annotate GFF files

Use gffutils to:

automatically fix start > end issues with gff
annotate each gff with gene_id= in attributes field of all children records of a gene entry
optionally add more specific annotations in attributes (up, dn, se exons for SE-style events)

Use annotated GFF files as a substitute for current annotations on website.

Add `which_miso`

That identifies:

Current MISO installation
Default settings file
Python version that is used.
tagBam if there optionally

GFF IDs don't correspond to exon start/stops

Hello Yarden et al,
This is more of a feature request than a bug.

I'm trying to understand the ID scheme of the provided gff3 files. It says in the documentation as an example, that the ID of one SE entry was "arbitrarily" chosen to be the coordinates of the 5' upstream exon, the SE itself, and its 3' downstream exon. However, I don't see this in the current SE.hg19.gff3 file:

(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/SE.hg19.gff3 | head
chr1    SE      exon    16854   17055   .       -       .       ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.dn;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1    SE      exon    17233   17742   .       -       .       ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.se;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1    SE      exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.up;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1    SE      exon    16854   17055   .       -       .       ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B.dn;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1    SE      exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B.up;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1    SE      exon    17233   17368   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A.dn;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1    SE      exon    17606   17742   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A.se;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1    SE      exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A.up;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1    SE      exon    17233   17368   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B.dn;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1    SE      exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B.up;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-

For example, the first exon is on the negative strand and has a start and stop of 16854 and 17055. However, its ID is chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.dn, which doesn't include either of those numbers!

This has been especially confusing when attempting to interpret MISO output, and going to the middle chromosome location in the ID, and finding no reads there. But the location specified by the start and stop columns in the original .gff3 file are correct, (which is comforting) but it's kind of a pain to have to grep for this arbitrary ID every time.

Is it possible for these .gff3 files to be updated such that the ID matches the chromosome location?

FWIW, this seems to also be an issue in A3SS.hg19.gff3:

(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/A3SS.hg19.gff3 | head
chr1    A3SS    exon    15796   15947   .       -       .       ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.A.coreAndExt;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.A;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1    A3SS    exon    16607   16765   .       -       .       ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.A.up;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.A;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1    A3SS    exon    15796   15942   .       -       .       ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.B.core;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.B;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1    A3SS    exon    16607   16765   .       -       .       ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.B.up;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.B;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1    A3SS    exon    17233   17742   .       -       .       ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.A.coreAndExt;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.A;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1    A3SS    exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.A.up;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.A;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1    A3SS    exon    17233   17368   .       -       .       ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.B.core;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.B;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1    A3SS    exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.B.up;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.B;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1    A3SS    exon    18268   18379   .       -       .       ID=chr1:8776:14754:-@chr1:8232|8242:8131:-.A.coreAndExt;Parent=chr1:8776:14754:-@chr1:8232|8242:8131:-.A;gid=chr1:8776:14754:-@chr1:8232|8242:8131:-
chr1    A3SS    exon    18913   24891   .       -       .       ID=chr1:8776:14754:-@chr1:8232|8242:8131:-.A.up;Parent=chr1:8776:14754:-@chr1:8232|8242:8131:-.A;gid=chr1:8776:14754:-@chr1:8232|8242:8131:-

A5SS.hg19.gff3:

(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/A5SS.hg19.gff3 | head
chr1    A5SS    exon    17233   17368   .       -       .       ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.A.dn;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.A;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1    A5SS    exon    17526   17742   .       -       .       ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.A.coreAndExt;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.A;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1    A5SS    exon    17233   17368   .       -       .       ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.B.dn;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.B;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1    A5SS    exon    17606   17742   .       -       .       ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.B.core;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.B;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1    A5SS    exon    16854   17055   .       -       .       ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.A.dn;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.A;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1    A5SS    exon    17606   18061   .       -       .       ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.A.coreAndExt;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.A;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1    A5SS    exon    16854   17055   .       -       .       ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.B.dn;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.B;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1    A5SS    exon    17915   18061   .       -       .       ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.B.core;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.B;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1    A5SS    exon    14363   16765   .       -       .       ID=chr1:6918:6739|6721:-@chr1:4226:6628:-.A.dn;Parent=chr1:6918:6739|6721:-@chr1:4226:6628:-.A;gid=chr1:6918:6739|6721:-@chr1:4226:6628:-
chr1    A5SS    exon    16858   17055   .       -       .       ID=chr1:6918:6739|6721:-@chr1:4226:6628:-.A.coreAndExt;Parent=chr1:6918:6739|6721:-@chr1:4226:6628:-.A;gid=chr1:6918:6739|6721:-@chr1:4226:6628:-

MXE.hg19.gff3:

(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/MXE.hg19.gff3 | head
chr1    MXE     exon    764383  764484  .       +       .       ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A.up;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1    MXE     exon    776580  776753  .       +       .       ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A.mxe1;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1    MXE     exon    787307  788090  .       +       .       ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A.dn;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1    MXE     exon    764383  764484  .       +       .       ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B.up;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1    MXE     exon    783034  783186  .       +       .       ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B.mxe2;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1    MXE     exon    787307  788090  .       +       .       ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B.dn;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1    MXE     exon    1027371 1027483 .       -       .       ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B.dn;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
chr1    MXE     exon    1041336 1041429 .       -       .       ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B.mxe2;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
chr1    MXE     exon    1051440 1051736 .       -       .       ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B.up;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
chr1    MXE     exon    1027371 1027483 .       -       .       ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.A.dn;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.A;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-

RI.hg19.gff3:

(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/RI.hg19.gff3 | head
chr1    RI      exon    17233   17742   .       -       .       ID=chr1:7464:7605:-@chr1:7096:7227:-.A.withRI;Parent=chr1:7464:7605:-@chr1:7096:7227:-.A;gid=chr1:7464:7605:-@chr1:7096:7227:-
chr1    RI      exon    17233   17364   .       -       .       ID=chr1:7464:7605:-@chr1:7096:7227:-.B.dn;Parent=chr1:7464:7605:-@chr1:7096:7227:-.B;gid=chr1:7464:7605:-@chr1:7096:7227:-
chr1    RI      exon    17601   17742   .       -       .       ID=chr1:7464:7605:-@chr1:7096:7227:-.B.up;Parent=chr1:7464:7605:-@chr1:7096:7227:-.B;gid=chr1:7464:7605:-@chr1:7096:7227:-
chr1    RI      exon    17233   17742   .       -       .       ID=chr1:7469:7605:-@chr1:7096:7231:-.A.withRI;Parent=chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7469:7605:-@chr1:7096:7231:-
chr1    RI      exon    17233   17368   .       -       .       ID=chr1:7469:7605:-@chr1:7096:7231:-.B.dn;Parent=chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7469:7605:-@chr1:7096:7231:-
chr1    RI      exon    17606   17742   .       -       .       ID=chr1:7469:7605:-@chr1:7096:7231:-.B.up;Parent=chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7469:7605:-@chr1:7096:7231:-
chr1    RI      exon    17606   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-.A.withRI;Parent=chr1:7778:7924:-@chr1:7469:7605:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-
chr1    RI      exon    17606   17742   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-.B.dn;Parent=chr1:7778:7924:-@chr1:7469:7605:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-
chr1    RI      exon    17915   18061   .       -       .       ID=chr1:7778:7924:-@chr1:7469:7605:-.B.up;Parent=chr1:7778:7924:-@chr1:7469:7605:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-
chr1    RI      exon    14407   16765   .       -       .       ID=chr1:4833:6628:-@chr1:4270:4692:-.A.withRI;Parent=chr1:4833:6628:-@chr1:4270:4692:-.A;gid=chr1:4833:6628:-@chr1:4270:4692:-

And TandemUTR.hg19.gff3:

(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/TandemUTR.hg19.gff3 | head
chr19   TandemUTR       exon    10663759        10664625        .       -       .       ID=chr19:10525223:10525625:-@chr19:10524759:10525222:-.A.coreAndExt;Parent=chr19:10525223:10525625:-@chr19:10524759:10525222:-.A;gid=chr19:10525223:10525625:-@chr19:10524759:10525222:-
chr19   TandemUTR       exon    10664223        10664625        .       -       .       ID=chr19:10525223:10525625:-@chr19:10524759:10525222:-.B.core;Parent=chr19:10525223:10525625:-@chr19:10524759:10525222:-.B;gid=chr19:10525223:10525625:-@chr19:10524759:10525222:-
chr1    TandemUTR       exon    227918925       227920091       .       -       .       ID=chr1:225986625:225986714:-@chr1:225985548:225986624:-.A.coreAndExt;Parent=chr1:225986625:225986714:-@chr1:225985548:225986624:-.A;gid=chr1:225986625:225986714:-@chr1:225985548:225986624:-
chr1    TandemUTR       exon    227920002       227920091       .       -       .       ID=chr1:225986625:225986714:-@chr1:225985548:225986624:-.B.core;Parent=chr1:225986625:225986714:-@chr1:225985548:225986624:-.B;gid=chr1:225986625:225986714:-@chr1:225985548:225986624:-
chr7    TandemUTR       exon    89861938        89866931        .       +       .       ID=chr7:89699874:89703121:+@chr7:89703122:89704867:+.A.coreAndExt;Parent=chr7:89699874:89703121:+@chr7:89703122:89704867:+.A;gid=chr7:89699874:89703121:+@chr7:89703122:89704867:+
chr7    TandemUTR       exon    89861938        89865185        .       +       .       ID=chr7:89699874:89703121:+@chr7:89703122:89704867:+.B.core;Parent=chr7:89699874:89703121:+@chr7:89703122:89704867:+.B;gid=chr7:89699874:89703121:+@chr7:89703122:89704867:+
chr3    TandemUTR       exon    111710568       111712215       .       +       .       ID=chr3:113193258:113193388:+@chr3:113193389:113194905:+.A.coreAndExt;Parent=chr3:113193258:113193388:+@chr3:113193389:113194905:+.A;gid=chr3:113193258:113193388:+@chr3:113193389:113194905:+
chr3    TandemUTR       exon    111710568       111710698       .       +       .       ID=chr3:113193258:113193388:+@chr3:113193389:113194905:+.B.core;Parent=chr3:113193258:113193388:+@chr3:113193389:113194905:+.B;gid=chr3:113193258:113193388:+@chr3:113193389:113194905:+
chr20   TandemUTR       exon    6055491 6057818 .       -       .       ID=chr20:6004667:6005818:-@chr20:6003491:6004666:-.A.coreAndExt;Parent=chr20:6004667:6005818:-@chr20:6003491:6004666:-.A;gid=chr20:6004667:6005818:-@chr20:6003491:6004666:-
chr20   TandemUTR       exon    6056667 6057818 .       -       .       ID=chr20:6004667:6005818:-@chr20:6003491:6004666:-.B.core;Parent=chr20:6004667:6005818:-@chr20:6003491:6004666:-.B;gid=chr20:6004667:6005818:-@chr20:6003491:6004666:-

Support overhang length in the C code.

Handle biological replicates automatically

Hi Yarden,

What about something like this: http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1318514284 for a tack on module at the end to handle biological replicates for calling the event-level differential splicing? I think you might get more uptake of MISO if it handled replicates automatically.

Replicate on samples

Hi Yarden,

I have subscribed to the mail list but there is still no confirmation so I ask the question here.

MISO run_miso.py --compare-samples perform pairwise comparison. If I have replicate on the samples, what is the best strategy to combine the results?

Marco

Handle BAM files with unaligned reads

Handle BAM files that have no CIGAR string (i.e. are unaligned)

Allow mixed iterations number comparisons

Trivial change to hypothesis_test.py: allow sample comparison between two samples that were running using different no. iterations/burn-in/lag parameters, i.e. make no assumptions about how many MCMC samples were produced.

`miso` error: "Import: unable to open X server `' @ import.c/ImportImageCommand/359" ...

Hello,
Using miso on our cluster, I get:

$ miso
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
/home/yeo-lab/software/bin/miso: line 10: from: command not found
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
/home/yeo-lab/software/bin/miso: line 20: from: command not found
/home/yeo-lab/software/bin/miso: line 21: from: command not found
/home/yeo-lab/software/bin/miso: line 22: from: command not found
import: unable to open X server `' @ import.c/ImportImageCommand/359.
/home/yeo-lab/software/bin/miso: line 25: syntax error near unexpected token `('
/home/yeo-lab/software/bin/miso: line 25: `miso_path = os.path.dirname(os.path.abspath(__file__))'

I thought it might have been some incorrect compilation on our server-side, so I installed it in an environment where I have total control (my laptop), but I get the same error:

$ git clone [email protected]:yarden/MISO
$ cd MISO
$ python setup.py build ; sudo python setup.py install
$ sudo miso
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 5: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 6: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 7: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 8: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 9: import: command not found
from: can't read /var/mail/collections
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 12: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 14: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 15: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 16: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 17: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 18: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 19: import: command not found
from: can't read /var/mail/misopy.parse_csv
from: can't read /var/mail/misopy.settings
from: can't read /var/mail/misopy.settings
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 23: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 25: syntax error near unexpected token `('
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 25: `miso_path = os.path.dirname(os.path.abspath(__file__))'

This is the exact same error as I get when I run just plain miso, without sudo. I tried sudo because I thought the error with can't read /var/mail/misopy.parse_csv might be because of permissions.

Please let me know how I may correctly install MISO.

Thank you,
Olga

What mapper does MISO supports?

I tried to run MISO to estimate insert size and compute-genes-psi

With identical parameters, annotation file provided by MISO and dataset.

Both insert size stimate and compute psi failed for BAM file generated from MapSplice and SpliceMap (both latest version). Only Tophat output's BAM run smoothly.

e.g. for SpliceMap and MapSplice's BAM, during compute-genes-psi, no files are output to output-directory. It always shows "only 0 reads in gene, skipping...."

Would like to ask which reads mapper were tested?

Thanks.

yarden / miso Goto Github PK

miso's People

Contributors

Stargazers

Watchers

Forkers

miso's Issues

Recommend Projects

Recommend Topics

Recommend Org