Question: Filter Fastq file by seq
1
gravatar for ta_awwad
4 months ago by
ta_awwad220
Frankfurt am Main
ta_awwad220 wrote:

Dear All: Does anyone know an efficient tool or script that removes certain reads with from Fastq file when it matches specific sequence? this means : if the reads contain my sequence so the entire read should be completely removed from the FASTQ file.

Many many thanks

R bioconductor ngs python • 235 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by ta_awwad220
1

Your question is similar to this one How to remove reads from fastq flle that match to a set of reads in my fasta file?

ADD REPLYlink written 4 months ago by Bastien Hervé4.4k
6
gravatar for finswimmer
4 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

Use seqkit grep:

$ zcat input.fq.gz | seqkit grep -v -s -i -p aggcg

This will remove all reads containing "aggcg".

ADD COMMENTlink written 4 months ago by finswimmer11k

thank you so much .. is there any option to remove the read of the same fragment from both paired-end FASTQ?

ADD REPLYlink modified 4 months ago • written 4 months ago by ta_awwad220
1

You could use repair.sh from BBtools to remove the corresponding paired read after removing your reads of interest in one of the files:

$ repair.sh in=input_1.fq.gz in2=input_2.fq.gz out=out_1.fq.gz out2=out_2.fq.gz
ADD REPLYlink written 4 months ago by finswimmer11k

this is awesome .. thank you so much

ADD REPLYlink written 4 months ago by ta_awwad220
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