paired-end reads in BBMap randomreads.sh

Question

[grant.hovhannisyan]

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 ?

Answer 1

[GenoMax]

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.

[grant.hovhannisyan]

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

[Charles Yin]

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