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Old 02-28-2011, 01:29 AM   #1
EGrassi
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Default IDs, standard format?

Hi,

I was wondering, now that SRA isn't available anymore, if the format that the sra toolkit adopted for the IDs of the reads will still be used or not.
Is there any effort to define the fastq format more precisely? About the IDs every different manufacturer uses its format right now?

Thanks,
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Old 02-28-2011, 05:19 AM   #2
maubp
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It is even worse, some manufacturers use different read naming conventions for different versions of their sequencer/software. For instance,
http://seqanswers.com/forums/showthread.php?t=8895

We tried to define the (sequence space) FASTQ format in this paper, but deliberately avoided the issue of the read names. Much like FASTA files, there are countless different naming conventions out there

Last edited by maubp; 02-28-2011 at 05:20 AM. Reason: typo
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Old 02-28-2011, 05:33 AM   #3
EGrassi
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Thanks for your reply. That paper was really useful, expecially regarding qualities...
As long as ID's are really redundant it is a shame that a single standard format isn't defined (or at least some of them, well documented)...it would help compression software performances, for instance.
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