Formatting BAM file and GTF file for feature counts
I am trying to format the identifiers in my BAM file to match with the GTF file. I used Samtools: IdxStats tool on my BAM file and I got the following output: https://ibb.co/10rT9tL I am getting zero counts for RNA seq reads after using featurecount tool in galaxy. I suspect there is some problem with chromosome identifiers in BAM file and GTF file. Can someone guide me in making the identifiers same for both files.
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abhilashtripathi10 •
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These situations almost always indicate a discrepancy between chromosome identifiers in your BAM and GTF files.
Since you are working with Galaxy you may want to post this question to Galaxy help forum for topical help.
Thank you for redirecting.