FastQC Illumina Universal Adaptors present

Question

[williamsbrian5064]

Hi

I just received some RNA-Seq data. When I run FastQC on the files, it appears that there are a decent amount of Illuminia universal adaptors present. Some of the samples up to 30%? I was wondering how to get ride of those adaptors?

Thanks

Answer 1

[Devon Ryan]

You can use a trimmer like "Trim Galore!", trimmomatic, or cutadapt. "Trim Galore!" has the benefit of auto-detecting the appropriate adapter sequence to trim (granted, you already know the sequence for these samples, but for the next time you get samples...).

Answer 2

[GenoMax]

By using a scanning/trimming program. I will link bbduk.sh from BBMap suite. There are multiple other options like trimmomatic, cutadapt etc.

Answer 3

[h.mon]

There are many programs to perform the task: BBDuk, Trimmomatic, SeqyClean, CutAdapt, TrimGalore, and others. I personally use BBDuk.

There are many posts about the subject, and many, many resources over the web - a search will lead you to very interesting sites.