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 ?
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grant.hovhannisyan
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.
Thanks @genomax! Very helpful. Quite intuitive, but would be nice to include it in the manual.
Very helpful. Thanks! I was looking for a tool to generate pair-end reads from assembled genome. This helps a lot.
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