Illumina adaptor to be trimmed from fastq RNAseq files

Question

[ebrahimiet]

Hi

Which Adaptor (and any other sequence) needs to be trimmed from RNASeq fastq data generated by Illumina TruSeq stranded mRNA Sample Preparation kit

Thanks

[Sej Modha]

Here is a nice tutorial and explanation about Illumina adaptors. You can use trim_galore to remove TrueSeq adaptors. Illumina adaptors explanation

Answer 1

[GenoMax]

BBMap suite (pure java, runs on WIn,macOS,linux) includes a file which contains all commonly used adapter sequences. You don't need to single out TruSeq adapters but can use entire (adapters.fa) file to scan your sequences with. bbduk.sh is the program you would want to use. adapters.fa file is in resources directory in bbmap source. See this thread for usage explanation.

Answer 2

[Jiacheng]

It is recommended to scan possible adapters and trim the exact adapter, rather than to trim all possible adapter sequences because the latter would over-trim a lot of sequences.

I'd recommend atria to determine and trim the adapter sequences. It is a cutting-edge trimmer with exceptional precision and speed.

Eg: Finding adapters

atria --detect-adapter -r reads.fastq [...]

Trimming single-ended fastq:

atria -r reads.fastq -a DETECTED_ADAPTER

Trimming paired-ended fastq:

atria -r read1.fastq -R read2.fastq -a DETECTED_ADAPTER1 -A DETECTED_ADAPTER2