Hi. Question about testing data I'm trying to writ...
# nf-test
u
Hi. Question about testing data I'm trying to write a module RMATS, processing RNAseq BAM files. This module has options for • single end vs paired-end reads • forward vs reverse vs unstranded/auto • additional options that don't depend on the library read type My understanding is that I should check that all options work when writing tests. I don't need to test all combinations. So I need to check read type twice (paired vs single), and read direction three times (forward, reverse, unstranded). I don't need to do all 6 combinations. Is that correct? I was looking at the human Illumina bams, and it seems like there is only paired-end RNA https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.bam - have I got that right? Is there any single-end RNA I've missed? Is the GTF file to use with this RNA https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/genome/genome.gtf? Thank you Uri David
If this is listed somewhere, you can just send me the link, but I couldn't find it in the readme in the homo_sapiens directory. Sorry!