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Old 04-10-2014, 07:47 AM   #1
shadow19c
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Location: france

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Default Demultiplexing qseq

Hello everyone I received data from Illumina sequencing into qseq files from different LANE.

And barcode for different samples.

SO I tried to transform my qseq files into fastq and then use fastx_barcode_splitter.pl to demultiplex by the barcode tag, but I am retrieving less reads.
I want to know if there is another strategy to demultiplex.


Best Regards,

Last edited by shadow19c; 04-10-2014 at 11:58 PM.
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Old 04-10-2014, 02:24 PM   #2
luc
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How many fastq files with reads do you have per lane? Did you use barcoded Truseq adapters or what type of adapters? Did you provide the barcode data in the correct orientation (perhaps the reverse complement should be used in your case?
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Old 04-11-2014, 12:04 AM   #3
shadow19c
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Hello,
So i have 20 .qseq files for each lane (3 Lanes).
So I transformed my 20 qseq files into one fatsq file, finnaly I have 3 fastq.

What do you mean
Quote:
the reverse complement should be used in your case
Best Regards,
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Old 04-13-2014, 07:41 AM   #4
sklages
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I have a tiny perl script here doing this job, qseq to fastq. PM me if you are interested.

best,
Sven
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Old 07-24-2014, 01:15 AM   #5
inesdesantiago
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Hi luc,
In which ocasions should one use the reverse complement?
I am looking at demultiplexing some data, and there are NO reads matching my barcodes. When I run FASTQC it seams like there are multiple sequences that would match the reverse complement of the barcode.
please have a look at my post: http://seqanswers.com/forums/showthread.php?t=45234

thanks
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Old 07-24-2014, 01:34 AM   #6
mastal
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Hi Ines,

Have a look at the following webpage from U. Texas at Austin, it may help.


https://wikis.utexas.edu/display/GSAF/454+-+all+flavors
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