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Old 07-19-2010, 05:45 AM   #1
Bruins
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Default qseq format question [Solved]

Hi all,

Bustard (pipeline 1.5) produces _qseq.txt files. These are the columns: machine name, run number, lane number, tile number, x and y coordinates of the clusters, index, read number, sequence, per base phred64 score and whether the read passed filtering.

All are clear to me except the index. Am I correct in assuming that the index represents the cycle number?

Another question. I read that the GAII has 100 tiles per lane. But I have 120 qseq files per lane. How come?

Many thanks!

Last edited by Bruins; 07-20-2010 at 02:53 AM. Reason: marked solved
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Old 07-19-2010, 06:56 AM   #2
kmcarr
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Quote:
Originally Posted by Bruins View Post
Hi all,

Bustard (pipeline 1.5) produces _qseq.txt files. These are the columns: machine name, run number, lane number, tile number, x and y coordinates of the clusters, index, read number, sequence, per base phred64 score and whether the read passed filtering.

All are clear to me except the index. Am I correct in assuming that the index represents the cycle number?
No, the index is not related to cycle number. The index field is used if you had pooled samples and used Multiplex ID (MID) tags. After identifying the ID tag in the index read (or index portion of read 1) the MID sequence will be recorded in the index field. If MID tags are not used the index field is always 0 (zero). For example, if a read from a pooled sample had the MID tag "ATAT" associated with it, its qseq line would be:

Code:
HWUSI-EAS1599 0019 1 1 1097 3011 ATAT 1 <seqread> <qual> 1
Quote:
Another question. I read that the GAII has 100 tiles per lane. But I have 120 qseq files per lane. How come?

Many thanks!
The latest model of the instrument, the GAIIx, collects 120 tiles per lane.

Last edited by kmcarr; 07-20-2010 at 04:26 AM. Reason: fix typo
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Old 07-19-2010, 07:08 AM   #3
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or...

Is it the index of a multiplexed sample, and 0 if no multiplexing? (like in the fastq format, see the wiki)
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Old 07-20-2010, 02:52 AM   #4
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I see I cross posted. Sorry kmcarr.

Thank you for your explanation!
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