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Old 11-08-2010, 12:18 AM   #1
enna80
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Default creating Roche's sff files

Hello,

does anybody knows if *.sff files can be created for example from Roche's *.qual and *.fna files?

Have a nice day, enna80
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Old 11-08-2010, 01:38 AM   #2
maubp
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The short answer is no, because you won't have the flow space information. You can fake this, but why bother? The Roche Newbler tools accept FASTA+QUAL as input don't they (as well as SFF)?
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Old 11-08-2010, 01:57 AM   #3
enna80
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Thank you!

Jup, just as i thought.

Well, problem is that the NCBI's Sequence Read Archive (SRA) will only take *.sff but for one sample we do not have them.

Best
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Old 11-08-2010, 02:06 AM   #4
maubp
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The NCBI certainly won't want an SFF file with faked flow information.

I suggest you email the SRA to explain your situation, but first try to talk to your sequencing center again about getting the SFF files (and in future, insist on them).
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Old 11-08-2010, 06:29 AM   #5
kmcarr
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Quote:
Originally Posted by enna80 View Post
Thank you!

Jup, just as i thought.

Well, problem is that the NCBI's Sequence Read Archive (SRA) will only take *.sff but for one sample we do not have them.

Best
While they certainly prefer the SFF file, they also will accept FASTQ files if that is all you are able to provide. A FASTQ can be created from the .fna & .qual files.
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Old 11-10-2010, 06:30 AM   #6
enna80
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Thank you dear all.

Indeed SRA prefers *.sff but meanwhile I found out, that they would also help you out, if you only can provide *.fna and *.qual.

I was also able to get all *.sffs now. The problem was a bug in the 2.0.00.20 software version of the 454 sequencer, which did not report the same IDs in the *.fna and the *.sff ...
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