ylab-hi / scanneo2 Goto Github PK

From the .tests/integration/config_basic/config.yaml
Do you know how I can get these files to test it?
TESLA_9_2.fastq.gz
TESLA_10_2.fastq.gz
TESLA_11_2.fastq.gz

The workflow/envs/optitype.yml environment is limited to NUMEXPR_MAX_THREADS" (64). This applies only when setting the threads number higher than 64.

Error.  nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)

Needs to be either increased or limited to 64 (hla typing)

I want to use the compile.py module.
However, in the repo, I can not found the description that illustrate where I can download the peptide.fasta
https://github.com/ylab-hi/ScanNeo2/blob/52a3818ec3189af502f18eba6b6a1a69b9b3a8c3/workflow/rules/prioritization.smk#L58C4-L58C43

Missing input data causes:

MissingInputException in rule fastqc_forward in file /projects/b1171/sej9799/GBM_analysis/ScanNeo2/workflow/rules/preproc.smk, line 35:
Missing input files for rule fastqc_forward:
output: results/SRR8281248/rnaseq/qualitycontrol/rna_tumor_R1_fastqc_raw.html, results/SRR8281248/rnaseq/qualitycontrol/rna_tumor_R1_fastqc_raw.zip
wildcards: sample=SRR8281248, seqtype=rnaseq, group=rna_tumor
affected files:
../GBM/SRR8281248_1.fastq

Should be caught differently

In ran on the star 2.7.1a star aligner. The option --chimOutType is not set correctly when I ran it showed me the conflict options.
https://github.com/ylab-hi/ScanNeo2/blob/main/workflow/rules/align.smk#L33C1-L33C34

EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions
SOLUTION: re-run with --chimOutType Junctions

However, the pipeline already sets with --chimOutType WithinBAM HardClip.
Currently, I replace the option as recommended automatically by the software.
Can you check on the current smk align rule. If it is not set correctly, please update the pipeline.

I tested on the test dataset of nextneopi (https://github.com/icbi-lab/nextNEOpi). I has a similar session for using the arriba to get the fusion genes. From those fusion genes, it can get the peptides that are possible to be the neoantigens.

There peptides with 8 amino acids:
PTEN - AC063965.1(21548),MED6P1(31892) MFSGGTCm FSGGTCmg SGGTCmgr GGTCmgrc GTCmgrcm TCmgrcmq Cmgrcmqt mgrcmqty grcmqtyp rcmqtypk cmqtypkv mqtypkvq qtypkvqg typkvqgs#Fusion-out-of-frame#high#yes#chr10:87952259#chr10:88016243#11#1#0#.#.

Your peptides with 8 amino acids:
MFSGGTCm

Is there anything wrong related to my test. Or your pipeline is focused on getting only this peptide rather than getting too much peptides sequence to achieve 37/38 active neoantigens on TELSA dataset?

Hi, I'm new to snakemake, and have no idea of submitting Scanneo2 jobs to HPC. Any instructions would be very helpful! Thanks!

Regards,
Xiao

When I ran spladder in the altsplicing task. It is lacked of parallel option that slows the process.
https://github.com/ylab-hi/ScanNeo2/blob/main/workflow/rules/altsplicing.smk#L17C1-L24C39
Just add --parallel <cpus>

Related to Ensembl/ensembl-vep#1332

Input should be splitted by chromosome...

It seems that rules which include /tmp need to be executed again when the workflow is not finished/aborted. The reason for that is /tmp as input which then causes the rule to be executed again since it has been changed (in later rules).

Is it possible?
Can targeted sequencing data be input file?

we have WTS & targeted sequencing file..
please let me know can i use this...

Best,

BAMfiles probably need to be QNAME sorted (rather than coordinate sorted) when splitting them

I reviewed the publication:
https://academic.oup.com/bioinformatics/article/39/11/btad659/7330407
I think that the pipeline used both bam files from RNAseq and DNAseq to call for the long indel. The bam file from the figure shows me it is only from the RNAseq bam file. If there is anything wrong, please let's me know.

A similar routine as for RNA-seq data required for BWA alignment for the DNA-seq path (when input is BAM file)