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Filter fastq file by first two base pairs

Hi, I have the fastq file example.fq and I would like to get only reads that start with a TG. Does anybody have advice for how to do this? I've been searching and and all the filtering systems I've seen look at read length or elements in the read id, but not in the sequence.

Thank you!

fastq
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updated by Ram Ram • written by Jautis Jautis

3 answers 

gunzip -c file.fastq.gz |\
    paste  - - - -  | awk -F '\t' '($2 ~ /^[Tt][Gg]/)' | tr "\t" "\n"
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Works like a charm, thank you! Do you think you could explain how it works?

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written by Jautis Jautis

Another possibility, just having fun:

grep --no-group-separator -A2 -B1 '^TG' test.fq | grep --no-group-separator -A3 '^@HISEQ'

The reads ID in my fq file start with @HISEQ. Change @HISEQ with whatever your read IDs start with.

• 1 views • link
updated by Ram Ram • written by iraun iraun

With BBMap:

bbduk.sh in=example.fq out=filtered.fq k=2 literal=TG rcomp=f mm=f restrictleft=2

This will also work on fasta.

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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