Question: Do I need to remove adapter if FastQC showed no adapter content.
0
gravatar for jolin0701-dy
2.2 years ago by
jolin0701-dy60
jolin0701-dy60 wrote:

I am new to RNA seq analysis.

I ran FastQC and results showed there is no adapter content. But there are still some overrepresented sequences.

Do I still need to remove adapter?

If so, how can I find the adapter?

Thanks a lot!

rna-seq • 1.6k views
ADD COMMENTlink modified 2.2 years ago by genomax49k • written 2.2 years ago by jolin0701-dy60
3
gravatar for genomax
2.2 years ago by
genomax49k
United States
genomax49k wrote:

It does not hurt to pass your reads through a scan/trim program. If there is no adapters present, no changes would be made to the data. You will only expend some time but would be assured that the data is clean.
BBDuk.sh from BBMap, trimmomatic or cutadapt are all paired-end data aware scan/trim programs. You will find sequences of all commonly used adapters in "adapters.fa" file in the "resources" directory of BBMap. Trimmomatic/cutadapt may also provide adapter sequences.
Note: If you do have light adapter contamination (sounds like the case here) then most NGS aligners should be able to take care of it (soft clipping). So if you don't want to scan/trim, you could proceed with alignments.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax49k

Thanks a lot!! It is very useful ~~

ADD REPLYlink written 2.2 years ago by jolin0701-dy60

Agreed. Also as of bcl2fastq 2.17.1.14 adapter trimming can take place while creating the fastq file.

ADD REPLYlink written 2.2 years ago by Ian5.2k
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