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6.1 years ago
subhadipkundu81
•
0
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?
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.
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.