I am trying to analyze RNA-seq data in DESeq in Galaxy and wonder if anyone has a detailed instructions or work flow how DEseq can be used after alignment in galaxy. Any pointer should be helpful. Since it is galaxy question I have also posted similar question on galxay but though this area may have better coverage. Thanks
The only real workflow would be to put the alignment files through either htseq-count or featureCounts, then putting the resulting files into DESeq. For featureCounts you'll need to select the correct output format (make sure to use the "DESeq2 IUC compatible ..." one). If you have a specific question about this then just ask.
As an aside, we literally did a training on this today here in Freiburg. You can find the training material online here.
I am using htseq-count for making count tables to be used with deseq later, but i am getting error .. no exon found. tThe gff file of brassica juncea does not have feature exon.. what can I do to solve this problem?