quant mode and sexual chromosomes
seoanezonjic opened this issue · comments
Hi
I'm using STAR to quantify my RNAseq samples but I have a problem. A group of genes in sexual chromosomes is missing in final count table. I think that this is due to X and Y chromosomes share sequences and reads map in these regions always are tagged as multimapped. I guess that --quantMode skips these alignments and loses all the shared sexual genes in these chromosomes.
Are my guessing correct? Is there some workaround to this behavior? If my suppositions are true I think that the STAR manual should be very clear about this behavior with the sexual chromosomes and warn to the user. Other option could be to specify which htseq read mode count must be used to generate the count table.
Thank you in advance
Pedro Seoane