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ylab-hi / ScanNeo2

Snakemake-based computational workflow for neoantigen prediction from diverse sources
MIT License
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Aligned option using star #21

Closed nttg8100 closed 6 months ago

nttg8100 commented 6 months ago

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.

riasc commented 6 months ago

Hello,

is there a reason you are using 2.7.1a and not 2.7.10b (which is the one used by the snakemake star wrapper - should probably update to 2.7.11b)? Or are you not able to use conda? As the authors of STAR are mentioning here: https://github.com/alexdobin/STAR/issues/1288 It's possible to call --chimMultimapNmax with --chimOutType WithinBAM in recent versions. We need to have it within the BAM (mainly because of Arriba) and would lose information otherwise.

nttg8100 commented 6 months ago

I see. Thank you for your clarification. I thought it could be the STAR version issue so I provided above. Currently, I have been used the image from STAR 2.7.1a for calling gene expression, fusion and this alt splicing, exonic introns. I will update later for my pipeline to use a unique version of STAR. Thank you for your support.