huangyh09 / briekit Goto Github PK

Hi,
I want to filter the splicing event by briekit-event-filter funciton. But some error and warnings came out. The GTF and fa files were downloaded from ENSEMBL. I assume that briekit may not support the chromosome name without 'chr'.

Could you give me some suggestions to fix it?

Here is my code to generate splicing GFF file and filter them:

Gfa=~/genome/ensembl/release97/mus_musculus/dna_seq/Mus_musculus.GRCm38.dna.primary_assembly.fa
GeGtf=~/genome/ensembl/release97/mus_musculus/dna_anno/Mus_musculus.GRCm38.97.gtf
briekit-event -a ${GeGtf} -o ./AS_events
for type in A3SS A5SS MXE RI SE
do
    # lenient filtering
    briekit-event-filter -a ./AS_events/${type}.gff3.gz --anno_ref=${GeGtf} -r ${Gfa} -o ./AS_events/${type}_lenient.gff3.gz \
                         --add_chrom X,Y --as_exon_min 10 --as_exon_max 100000000 --as_exon_tss 10 --as_exon_tts 10 --no_splice_site
done

Here are the total number of rows of splicing annotation GFF files:

$ for file in AS_events/*gz; do zcat $file | wc -l; done
41839
22365
11961
16332
104048

The Information returned can be checked in here.

Hi there,

I was hoping to use briekit to generate a splicing event annotation file for t. I am getting the following error:

File "~/site-packages/briekit/events/event_maker.py", line 11, in import parseTables as parseTables ModuleNotFoundError: No module named 'parseTables'

I'm using python v2.7 and numpy 1.13.0 as per the recommendations in the manual.

Wondering how I might resolve this error? Thanks in advance!

Got a problem using briekit on rheMac10, for rheMac didn't have corresponding phastcon files. And it's too time-consuming to generate a new one. So can I just skip the final step "Extacting sequence feature for BRIE" to do brie-count or brie-quant?
Any advices might help. Thank you

Hello,

I am using briekit-events to extract splicing events from the human gencode v25 annotation file in gff3 format, which has over 55k genes. However, the output file has alternative splicing events of only 10k unique genes (only SE events) or 12k unique genes if all types of AS are taken into account. I did not perform any further filtering steps. Why is there such a big difference? How can I get all the splicing events for all the genes in gencode v25?

I've checked the file provided in brie2 documentation (https://sourceforge.net/projects/brie-rna/files/annotation/human/gencode.v25/) and it has roughly the same amount of unique genes.

I wonder if it might be because many genes have AS events that are not one of the 5 types that briekit is looking for (SE, RI, A3SS, A5SS or MXE). Could this be the reason?

Thank you very much in advance,
Nil

Hi,

I am using the "samples.csv.gz" file generated by brie (splicing quantification) as a "miso_files" input for the sashimi plot. However, no posterior plot is generated. You showed in the 'https://github.com/huangyh09/briekit/blob/master/sashimi_plot/settings/sashimi_settings_brie.txt' file that it is possible to do so. Any idea why?

Gabriel

hi, I got this error when I run
briekit-event -a /disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf -o /disk2/brie_rnasplicing_bc25/bc25_as/
Making GFF alternative events annotation...
Input annotation files: /disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf
Output dir: /disk2/brie_rnasplicing_bc25/bc25_as/
('Reading table', '/disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf')
Traceback (most recent call last):
File "/home/JHma/miniconda3/envs/RNASEQ/bin/briekit-event", line 11, in
load_entry_point('briekit==0.2.2', 'console_scripts', 'briekit-event')()
File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 175, in main
File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 69, in defineAllSplicing
File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 39, in prepareSplicegraph
File "build/bdist.linux-x86_64/egg/briekit/events/parseTables.py", line 85, in populateSplicegraph
File "build/bdist.linux-x86_64/egg/briekit/events/parseTables.py", line 64, in readTable_gff
UnboundLocalError: local variable 'exons' referenced before assignment
Could you help me? Thanks

HI,

thanks for this nice tool.
When I dont use Gencode gtf, I encounter errors.
for GRCh38.p13 from ensembl I get following error:

I already added chr as a prefix for the chromosome column, but still the same error.

Any suggestions?

hi,I got this error when I run
briekit-event-filter -a /path/to/A3SS.gff3.gz --anno_ref /path/to/gencode.vM22.annotation.gff3 -r /path/to/GRCm38.p6.genome.fa

5955 Skipped Exon events are input for quality check.
0 Skipped Exon events pass the qulity control.
Traceback (most recent call last):
File "xxxx/envs/briekit/bin/briekit-event-filter", line 10, in
sys.exit(main())
File "xxxx/miniconda2/envs/briekit/lib/python2.7/site-packages/briekit/events/event_filter.py", line 395, in main
g_idx, g_chr, g_start, g_stop = get_gene_idx(anno_out)
File "xxx/miniconda2/envs/briekit/lib/python2.7/site-packages/briekit/events/event_filter.py", line 41, in get_gene_idx
g_idx.append([now_g, last_g])
UnboundLocalError: local variable 'last_g' referenced before assignment