FastQC Illumina Universal Adaptors present

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

rna-seq genome next-gen assembly

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updated 8.5 years ago by h.mon 3.5K • | written 8.5 years ago by williamsbrian5064 55

3 answers

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...).

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written 8.5 years ago by Devon Ryan 10K

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

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written 8.5 years ago by GenoMax 16K

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.

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written 8.5 years ago by h.mon 3.5K

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