[Bioc-sig-seq] who have tag-clean software

[Steve Lianoglou]

Hi,

On Mon, Sep 12, 2011 at 2:01 PM, wang peter <wng.peter at gmail.com> wrote:
> dear sir or madam:
> who have tag-clean software?
> i want to compare the results by using R coding with the results by using
> software.
> what i will do include remove low quality reads and remove 3' adaptors

Look at the fastx_toolkit:
http://hannonlab.cshl.edu/fastx_toolkit/

In particular, you want to look at `fastx_clipper` to remove 3'adaters
and `fastq_quality_trimmer` to remove low scoring bases.

`cutadapt` is another tool that removes adapters as well:
http://code.google.com/p/cutadapt/

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact