[Bioperl-l] Working with SeqWithQuality

Cook, Malcolm MEC at stowers-institute.org
Thu Jun 19 11:37:20 EDT 2008


Michael,

If you happen to be working abi chromatogram files you can use perl's Bio::Trace::ABIF (c.f. CPAN) to do this directly easily without need for SeqWIthQUality objects.

???

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of michael watson (IAH-C)
Sent: Thursday, June 19, 2008 9:52 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Working with SeqWithQuality

Hi

I have fasta files and separate quality fasta files.  I understand all about constructing a SeqWithQuality object, that's the easy bit, but are there no functions for actually manipulating the sequence based on the quality values?  For example, trimming the ends where a moving window average quality does not go above a certain value, or masking areas with low quality?

Thanks
Mick

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