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