This is a test version of Biostars. For the public version, visit https://www.biostars.org.
excluding a particular gene (coordinates) from BAm

I want to exclude a particular gene (or coordinates of the gene) from aligned reads in a bam file. How can I do that. The reason is for quantitation of RNA-seq I want to exclude this particular gene

bam

1 answer

Just exclude that gene from your GTF file so it is not counted. If you already have the counts then delete the count row for that gene.

Log in to answer this question.