calling reads by size

[Pol8]

Hi everyone,

basic question: which is the best way to have a fasta file containing only the 21-long reads, starting from the cleaned 'total reads.fasta'?

Thanks

[GenoMax]

What sequencer platform is this for? You want to keep reads that are only 21-bp (or at least 21bp and longer)?

[Brian Bushnell]

Reformat can do that, like this:

reformat.sh in=reads.fasta out=21.fasta minlen=21 maxlen=21

[Pol8]

Only the 21 long. Mines are Illumina data.

[GenoMax]

Follow Brian's suggestion. You may have to indicate the following if you have fastq format files and want to keep them in that format.

reformat.sh in=reads.fastq out=21.fastq minlen=21 maxlen=21

This may work if you want them converted from fastq to fasta format:

reformat.sh in=reads.fastq out=21.fasta minlen=21 maxlen=21