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Thread | Thread Starter | Forum | Replies | Last Post |
Generating SFF files | Xterra | 454 Pyrosequencing | 8 | 10-31-2011 02:07 PM |
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The DNA extracted by kit contain only nucleus DNA? | bbsinfo | General | 5 | 04-21-2011 06:08 AM |
sff extract | dina | Bioinformatics | 3 | 03-01-2010 03:55 AM |
SFF: PE or not PE? That is my question. | dan | Bioinformatics | 4 | 12-29-2009 07:20 AM |
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#1 |
Member
Location: Dublin, Ireland Join Date: Sep 2009
Posts: 22
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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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#2 |
Member
Location: Cambridge, UK Join Date: Sep 2009
Posts: 37
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Have you tried 'sfffile -i'?
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#3 |
Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
Posts: 1,543
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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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#4 |
Member
Location: Dublin, Ireland Join Date: Sep 2009
Posts: 22
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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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Tags |
extract, plasmid, reads, sff |
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