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-   -   how to separate barcode libraries from csfasta and qual file (http://seqanswers.com/forums/showthread.php?t=13191)

lei 08-03-2011 08:12 AM

how to separate barcode libraries from csfasta and qual file
 
anyone knows about how to do that?
Thanks!

westerman 08-03-2011 08:34 AM

No need to do so. The libraries are already extracted by the machine, at least on the SOLiD 4 and SOLiD 3.

lei 08-03-2011 11:30 AM

really?I just got one csfasta and qual file including 8 libraries from the core facility. If so, I will ask them tomorrow.

westerman 08-03-2011 11:43 AM

Yes, ask them. Let us know what they say. Since the SOLiD has separate runs for the barcode, the F3 and the F5/R3 then these should separate into three different files and into different samples. We get (and give to our customers) files that are named like:

run00165_Stemredo_BC_000738_StemRedo_05.csfasta
run00165_Stemredo_F5-BC_000738_StemRedo_05.csfasta
run00165_Stemredo_F3_000738_StemRedo_05.csfasta

run00165_Stemredo_BC_000739_StemRedo_06.csfasta
run00165_Stemredo_F5-BC_000739_StemRedo_06.csfasta
run00165_Stemredo_F3_000739_StemRedo_06.csfasta

Plus associated qual and stats files; e.g.,

run00165_Stemredo_BC_QV_000738_StemRedo_05.qual
run00165_Stemredo_BC.stats

Note that there are three .csfasta files per sample.


It is possible to merge all data from the samples into one file. But, at the risk of critiquing another core facility, why do so?

songxifan 10-21-2011 07:38 PM

I'm having the same problem. I have four barcoded samples, but only got one csfasta and qual files. Did the ppl got the solution for the problem from ABI?
Thx!


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