Is there a way to map a portion of reads?

[jeow]

Hello,

I have a very large dataset and not enough disk space. Is there a way to map only a portion (say 10%) of the reads? I am using tophat to map but I cannot find any options to do this in the manual. Thanks!

[GenoMax]

You can sample a subset of the reads using reformat.sh from BBMap suite like this. Replace the NNN with number of reads you want.

$ reformat.sh in=reads.fq out=sampled.fq sample=NNN

Then align.

OR

you could use bbmap.sh (instead of tophat) and add the option "samplerate=0.1" to randomly select 10% of reads to map from your file.

[jeow]

Great! Thanks for the help.