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Old 02-27-2010, 09:20 PM   #1
Location: israel

Join Date: Sep 2009
Posts: 34
Default sff extract

How can I extract sff files? only in linux or windows is possible too?
dina is offline   Reply With Quote
Old 02-28-2010, 01:47 AM   #2
Location: uk

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This program will do the job. It works on Windows and linux so long as you have python installed.
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Old 02-28-2010, 05:56 AM   #3
Location: China

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you can try:

Usage: sffinfo [options...] [- | sfffile] [accno...]
-a or -accno Output just the accessions
-s or -seq Output just the sequences
-q or -qual Output just the quality scores
-f or -flow Output just the flowgrams
-t or -tab Output the seq/qual/flow as tab-delimited lines
-n or -notrim Output the untrimmed sequence or quality scores
-m or -mft Output the manifest text
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Old 03-01-2010, 03:55 AM   #4
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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bio-x is suggesting using the Roche tool sffinfo which comes with the "Newbler" package. Note that this is Linux only. See also getting Newbler.
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