Formatting BAM file and GTF file for feature counts
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9 months ago

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.

BAM FEATURECOUNTS RNA-Seq alignment • 358 views
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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.

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Thank you for redirecting.

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