[EMBOSS] Trim polyA from fastq files

[michael watson (IAH-C)]

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

Thanks
Mick

-----Original Message-----
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:
> Hello
>
> 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.

regards,

Peter Rice