[EMBOSS] Trim polyA from fastq files

[Peter]

On Thu, Oct 1, 2009 at 1:53 PM, michael watson (IAH-C)
<michael.watson at bbsrc.ac.uk> wrote:
>
> Hi Peter
>
> Thanks for that.
>
> Is it possible to preserve the fastq format?  My input was fastq, I also put .fastq as my output, but it only gave me straight fasta
>

Use "fastq-sanger" (or a variant), not just "fastq" which means
ignoring the qualities in EMBOSS.

http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in

Peter