I was trying to count the number of reads through HTSeq but failed.

[Raja_ishaq_Nabi_Khan]

The results of HTSeq is shown in plain image . What could be reason for this ?? Erroneous Gff file or erroneous Bam file? I am attaching here sorted report of the bam file ( green background) as well

[jennaj]

Does the GTF dataset contain any data lines with “exon” in the 3rd column? The error suggest that it doesn’t and you either need to modify the feature used for counting or find a more suitable GTF source.

Exon is the default feature considered by HTseq-count wrapped for Galaxy. Screenshot:

Please see the RNA-seq tutorials for example usage:

Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

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