Demultiplexing qseq

[shadow19c]

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,

[luc]

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?

[shadow19c]

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

the reverse complement should be used in your case

Best Regards,

[sklages]

I have a tiny perl script here doing this job, qseq to fastq. PM me if you are interested.

best,
Sven

[inesdesantiago]

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

[mastal]

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