I am going to have to analyze data obtained from AmpliSeq Technology (the full panel containing about 20,000 genes), and I was wondering whether I could use Galaxy for that.
I am currently using Galaxy for RNAseq analyses, but as I understand, I won't be able to use exactly the same tools to work with AmpliSeq data. Unfortunately, I could not find any workflow for AmpliSeq in Galaxy.
I learned that I will need to use TMAP aligner, which is available in the toolshed, but I was wondering what are the steps prior to the TMAP and what would be the steps after the TMAP - would they be different than after usual alignment for RNAseq?
Thank you very much!