Question

How to trim the adapter from paired end RNA-seq data

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2.7 years ago

Su • 0

Hi,

I am working with the Illumina paired-end data using Truseq stranded mRNA library prep kit. I would like to initially identify the adapter sequences present in the data, and trim the reads. I checked the data using Fastqc software and it showed no adapter was detected in the data. But, the report from the sequencing company said the read has not trimmed for the adapter. On the Illumina website, I searched for the sequencing adapter for this type of library kit to be trimmed, and a sequence was found. Besides that sequence, Illumina said trimming T overhang is required additionally for that library. I have no idea what to do with this data whether trimming is required or not and how to trim the T overhang. Is there any way to do this issue properly? Please assist me with this and let me know the tools to use.

Thank you, Su

RNA-seq Truseq stranded adapter trimming • 1.9k views

ADD COMMENT • link updated 2.7 years ago by stuart archer ▴ 140 • written 2.7 years ago by Su • 0

score 2 · Answer 1 · 2022-03-24

I am working with the Illumina paired-end data using Truseq stranded mRNA library prep kit. I would like to initially identify the adapter sequences present in the data, and trim the reads.

If you know the library used TruSeq kit then you don't need to identify sequences. They are available publicly (and in trimming programs mentioned below e.g. adapters.fa in resources directory in BBMap distribution).

Fastqc software and it showed no adapter was detected in the data.

That is certainly possible. Your data does not need to contain adapter sequences. Only if library inserts are shorter than the length of sequence cycles then adapter sequence will be present.

Most times aligners will be able to soft-clip any extraneous sequence present so technically you don't need to trim data unless you are going to do de novo assembly. In that case you would not want any extraneous sequence to be present.

You can trim the data (nothing will be removed if adapters are not present) using bbduk.sh (a guide is available: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ ), fastp or trimmomatic.