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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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Gene counts #18

Closed lukewgarratt closed 1 year ago

lukewgarratt commented 1 year ago

Hello, What is the best approach to also generate gene counts for the human alignments and summarise into a csv file? If I modify star_mapping-pe.cwl with "--quantmode GeneCounts" then that will try to generate counts for both the human and virus data, correct? I notice that the index run does not download gtf files or generate a geneInfo.tab that STAR expects to find. Thank you

lukewgarratt commented 1 year ago

Alright, I've created my own solution by incorporating the salmon steps from the first VIRTUS into a hybrid pipeline. Doesn't add too much computation time (gone from ~63 min per PE sample to ~70 min).

yyoshiaki commented 1 year ago

Thank you!