How to generate counts from my HISAT2 alignment (BAM file)?

First of all, can you tell me how necessary it is to generate read counts in an RNA-Seq differential expression analysis and what it is for? I’m working with the reference genome of Arabidopsis thaliana and paired-end data.

I checked the tools FeatureCounts and HTseq counts and both of them require a GTF file, but the Arabidopsis genome is not listed there, should I do my own GTF file with the whole genome or just with some genes?


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Hi Mario

Without a count table, you cannot do the differential gene expression analysis. You might want to read up on this in the training material:

For both htseq-count and featureCounts, you can provide your own GTF file. A possible source is here:

Even if you are interested in only a few genes, it is recommended to to the differential gene analysis on all genes, and select afterwards.

I hope this helps, Hans-Rudolf