RNA_calling.ipynb rsem_call error when using BAM files from STAR with wasp filter

cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium

https://cumc.github.io/xqtl-protocol/

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RNA_calling.ipynb rsem_call error when using BAM files from STAR with wasp filter #696

Open grennfp opened 11 months ago

grennfp commented 11 months ago

Running alignment with the STAR wasp option creates *toTranscriptome.out_wasp_qc.bam files. When running RSEM, the code expect the files to not include "_wasp_qc" in the name, causing an error.

gaow commented 6 months ago

@grennfp is this fixed now? It looks like a file naming issue that can be addressed with a bit of SoS/python syntax?