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how to removed the first two nucleotides from a fastq file (single-end)

"CAGE (cap analysis of gene expression; Table S1) was as described (Yang et al., 2011) and sequenced using a HiSeq 2000 (100 nt reads). After removing adaptor sequences and checking read quality using Flexbar 2.2 with the parameters of “-at 3 -ao 10 --min-readlength 20 --max-uncalled 70 --phred-pre-trim 10”, we retained only reads beginning with NG or GG (the last two nucleotides on the 5′ adaptor). We then removed the first two nucleotides and mapped the sequences to the mouse genome using TopHat 2.0.4. " This is the way the literature works, how do I write code to remove the first two nucleotides

cgae-seq fastq
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updated by cpad0112 cpad0112 • written by 17318598206 • 17318598206

multiple ways:

$ cutadapt -u 2 -o new.fastq input.fastq
$ seqkit subseq -r 3:-1 input.fastq -o new.fastq
$ sed -r '0~2 s/^.{2}//' input.fastq > new.fastq
$ awk '{print (NR%2 == 0 ? substr($0,3): $0)}' input.fastq > new.fastq
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written by cpad0112 cpad0112

You can use "HEADCROP" option in "Trimmomatic"

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written by reza reza

2 answers 

awk '{if(NR%2){print $0}else{print substr($0,3)}}' in.fq > out.fq
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written by 5heikki 5heikki

code to remove the first two nucleotides

You can use bbduk.sh from BBMap suite like this:

bbduk.sh -Xmx2g in=your.fq out=trimmed.fq forcetrimleft=2

A guide to use BBDuk is available.

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written by GenoMax GenoMax

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