What value shoould be filled at Choose Adapter Clip adapter sequences Galaxy

Question

[Kian]

I have a RNAseq data that i upload to usegalaxy and convert to Fastq format (fastq-dump). then i want to remove adapter sequence. With Clip tool in usegalaxy, there are a filed that should be fill with "Choose Adapter". how i can fill this filed? thanks

Answer 1

[Devon Ryan]

It's unclear which of the trimming tools you're using. Trim Galore! is in Galaxy and doesn't require specifying an adapter sequence (it'll generally figure that out for you).

However, I encourage you to skip the trimming step and simply use STAR (also available in Galaxy) to align your data. It will use local alignment, wherein adapter sequences will simply be soft-clipped.

[Kian]

Thanks Dear Ryan, Do you mean "RNA STAR" tool -Gapped-read mapper for RNA-seq data ? its needs the reference genome, as i work on the cow genome there are not this genome on the list.

[Devon Ryan]

You can upload whatever you have available (I assume your goal isn't to do assemble the transcriptome).