While using Featurecounts tool, I am getting zero counts for RNA seq reads, It can be due to unmatched chromosome identifiers in BAM and GTF file. Can someone please help me out in making the identifiers same for both the file?
Thank You
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The graphics have the chromosome ID in the first, but the gene IDs in the second. And it looks as if somewhat significant number of your reads did not map at all (might be expected – if you didn’t do QA on your reads before mapping, maybe consider doing some).
How to check for a match plus how to address mismatches are covered in these FAQs:
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
- Extended Help for Differential Expression Analysis Tools
Plus I added some tags to reach prior QA.
Let’s start from there. Since none of the gene IDs in the graphic are assigned, it is difficult to know if all genes had a count of “0” (could be a mismatch issue) or only some did (that could be some other format or even content issue). But check the IDs – it is important.