I want to remove the universal adapters as well as the index adapters in each data file of my RNAseq data in Galaxy. I know you can can specify exactly what sequence to remove by pasting in the sequence for the adapter sequence to be trimmed off in Trim Galore!. However, i would like to specify multiple sequences at the same time and i cant see an option for this in Trim Galore!
I can see that you are able to trim multiple sequences in Trimmomatic by uploading a Fasta of adapters to clip. I pasted in the universal adapter sequence and all of the possible index adapter sequences into Notepad each with a line separating them, i saved this file as a .txt file, uploaded it to galaxy and under Datatype changed it to Fasta. I then used this file in Trimmomatic under 'Fasta of adapters to clip' but it didn't work (i,e. the adapters weren't trimmed off). I also tried putting a '>' in front of each of the sequences in notepad as i read online somewhere to do this. However this also didn't work. I was wondering if anyone could tell me where i was going wrong?
Thanks so much!