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Old 07-15-2011, 02:48 AM   #1
Kasycas
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Default extracted sequences from sff

Hi,

Has anyone successfully extracted a subset of sequences by their read ID from an sff file? I'm trying to separate plasmid and chromosomal reads from a bacterial sequencing project and I've tried using cBar to pull apart which reads are which. Now it's a matter of testing if the assembly works better with the separated reads.

Thanks!

Kasycas
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Old 07-15-2011, 04:06 AM   #2
vadim
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Have you tried 'sfffile -i'?
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Old 07-21-2011, 11:16 AM   #3
maubp
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If you want a Galaxy based solution (and you have a local Galaxy install), I have two related tools which can do this for FASTA, FASTQ or SFF files (using Biopython internally).

Goto the Galaxy Tool Shed, http://usegalaxy.org/community and search for seq_filter_by_id and seq_select_by_id
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Old 07-21-2011, 02:26 PM   #4
Kasycas
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Thanks for the answers vadim and maubp, I'll give them a go. I hadn't realised Roche had this sfffile tool and Galaxy's a good option as well.
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