deMultiplex

[sivasubramani selvanayagam]

Dear Guys,

I would like to know is there any way I can extract the reads per sample from GBS fq file. I have a key file and a fq raw reads file. If not let me know the way to do it. I tried writing script to do so, but I faced some issues with that (Key barcode contains restriction site 4 bases, 2 barcodes in same read and so on).

Best,
Siva

[sivasubramani selvanayagam]

in continuation with the question asked:

 I would like to get the reads which are not being used in the TASSEL pipeline. How would I get that.

[JL265]

I'm also interested in the answer to this question, does TASSEL have a plugin to demultiplex reads from fastq.gz files into sample-specific files so that they can be deposited into NCBI Sequence Read Archive?

[Jeff Glaubitz]

You might want to try the FASTX-Toolkit:

http://hannonlab.cshl.edu/fastx_toolkit/

 

Best,

 

Jeff

 

--

Jeff Glaubitz

Project Manager

Biology of Rare Alleles in Maize and its Wild Relatives

National Science Foundation award IOS-1238014

http://www.panzea.org

Institute for Genomic Diversity

Cornell University

175 Biotechnology Bldg

Ithaca, NY 14853

Phone: 607-255-1386

jcg...@cornell.edu

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[JL265]

OK, thanks.  I'll look into that.