Tag: bulkRNAseq

mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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DEGs with uninsteresed sample files

DEGs with uninsteresed sample files 1 Hi all, I am working on some bulkRNAseq data from GEO and my sample description looks like this. I am interested in A vs B, A vs C and B vs C but I am not interested in sample D. My question is whether…

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