[EMBOSS] Trim polyA from fastq files
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Thu Oct 1 08:53:12 EDT 2009
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
From: Peter Rice [mailto:pmr at ebi.ac.uk]
Sent: 01 October 2009 13:10
To: michael watson (IAH-C)
Cc: 'emboss at emboss.open-bio.org'
Subject: Re: [EMBOSS] Trim polyA from fastq files
On 01/10/09 12:33, michael watson (IAH-C) wrote:
> I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format.
> Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file
Yes, but you need EMBOSS 6.1.0 to support FASTQ input.
There are also a couple of patches that are needed for some FASTQ files.
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