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][1] ?


  [1]: https://www.biostars.org/u/14684/
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.