Question: Filter Fastq file by seq
1
gravatar for ta_awwad
15 months ago by
ta_awwad260
Frankfurt am Main
ta_awwad260 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 • 616 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by ta_awwad260
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 15 months ago by Bastien Hervé4.5k
6
gravatar for finswimmer
15 months ago by
finswimmer13k
Germany
finswimmer13k 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 15 months ago by finswimmer13k

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

ADD REPLYlink modified 15 months ago • written 15 months ago by ta_awwad260
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 15 months ago by finswimmer13k

this is awesome .. thank you so much

ADD REPLYlink written 15 months ago by ta_awwad260
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