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Question: Is it important to perform Adapter sequence removal step?
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gravatar for k.ip
2.3 years ago by
k.ip • 10
Australia
k.ip • 10 wrote:

Hello,

Can I ask is it important to perform the adapter removal step, when I ran the RNA-seq fastq file with FastQc and it didn't pick up any over-represented sequences?

And how would I know what is the adapter sequences from my data file?

Thanks a lot for answering me.

Kind regards, Ken
rna-seq • 1.4k views
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modified 2.3 years ago by Devon Ryan • 1.9k • written 2.3 years ago by k.ip • 10
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gravatar for Devon Ryan
2.3 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

It never hurts to perform adapter trimming. Regarding the sequence, you'll need to ask whoever did the library preparation, though in practice "Trim Galore!" can usually detect this for you without issue.

If FastQC isn't showing anything then it's likely that the results won't be affected much by not trimming off adapters. However, since trimming doesn't take that long and many RNAseq aligners in Galaxy can't do local alignment you're get a bit better results if you do trim.
ADD COMMENT • link written 2.3 years ago by Devon Ryan • 1.9k
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