Question: paired-end reads in BBMap randomreads.sh
1
gravatar for grant.hovhannisyan
2.4 years ago by
grant.hovhannisyan2.0k wrote:

Hi Biostars,

How to set the names of two output files (corresponding to each mate) in randomreads.sh script of BBMap package?

Help page specifies the out=filename option but when doing like that I get only I file containing both mates. Omitting that option produced two files but with random names.

Here is the command I use:

randomreads.sh ref=C_glabrata_CBS138_current_chromosomes.fasta out=reads.fastq length=75 reads=100 coverage=1 replacenoref=t simplenames=t seed=-1 paired=t metagenome=t

Thanks

P.S. How can I tag Brian Bushnell ?

bbmap randomreads • 1.3k views
ADD COMMENTlink modified 2.4 years ago by genomax92k • written 2.4 years ago by grant.hovhannisyan2.0k
3
gravatar for genomax
2.4 years ago by
genomax92k
United States
genomax92k wrote:

You can do following with any additional options you need.

randomreads.sh ref=C_glabrata_CBS138_current_chromosomes.fasta out1=read1.fq out2=read2.fq paired=t addpairnum=t

If you use a single output name then the reads will be interleaved. You can separate them into two files using reformat.sh.

reformat.sh in=reads.fq out1=R1.fq out2=R2.fq

You had tagged @Brian the right way.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by genomax92k
1

Thanks @genomax! Very helpful. Quite intuitive, but would be nice to include it in the manual.

ADD REPLYlink written 2.4 years ago by grant.hovhannisyan2.0k

Very helpful. Thanks! I was looking for a tool to generate pair-end reads from assembled genome. This helps a lot.

ADD REPLYlink written 22 months ago by genebow160
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