RNASeq analysis base trimming

Question

[subhadipkundu81]

Hi I am trying to analyze my RNASeq data using apple terminal, I am stuck in analyzing base trimming, probably I have to download Fastx-toolkit for base trimming, how can I download it using commanad line in my apple terminal?

[GenoMax]

Do you have experience working on the command line? Have you done any analysis on command line before?

If the answer is no to both then I suggest that you take a look at this RNAseq data analysis pipeline. It would also help to familiarizie yourself with UNIX with this tutorial.

[h.mon]

Do not use Fastx-toolkit, it is really old and was developed when most NGS sequencing was single-end. It is a recurring question here at Biostars "why my mapping fails?", after trimming read1 and read2 files independently (most of the times with Fastx-toolkit) and feeding the now improperly paired reads to the mapping software.

Answer 1

[grant.hovhannisyan]

Try to use trimmomatic - it is java software so I guess you will be able to use form mac terminal (NOTE: you might need to install java first if you don't have it)