Question: Combine paired-end fastq files
0
gravatar for 112498262
5 weeks ago by
1124982620
1124982620 wrote:

I am trying to use SCARPA for scaffolding. I have been given two separate paired-end fastq files, one containing each forward read and the second containing the corresponding reverse reads. SCARPA requires the read data to be in a single fastq format, whereby the forward and reverse read of each pair are consecutive in the file.

How do I merge my two fastq files to one file in the required format?

Thanks :)

sequencing next-gen • 144 views
ADD COMMENTlink modified 5 weeks ago by genomax67k • written 5 weeks ago by 1124982620
1

That is called an interleaved fastq, so googling that should bring up some ideas.

ADD REPLYlink written 5 weeks ago by WouterDeCoster39k

Thank you so much. I used interleave-fastq, it worked a charm :)

ADD REPLYlink written 5 weeks ago by 1124982620
2
gravatar for genomax
5 weeks ago by
genomax67k
United States
genomax67k wrote:

Use a program from BBMap suite.

reformat.sh in1=R1.fq.gz in2=R2.fq.gz out=interleaved.fq.gz
ADD COMMENTlink written 5 weeks ago by genomax67k
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