I have had the same problem, and am also a newbie to NGS with Illumina.  The work-around I found was to download bowtie directly from the website, run it on your local computer, then upload the resulting SAM file for subsequent Galaxy-driven analysis.  Not optimal, I know, but if you are in a hurry...


On Tue, Apr 6, 2010 at 1:20 PM, Weng Khong Lim <wengkhong@gmail.com> wrote:
Hi all,

I'm new to next-gen sequencing, so please be gentle. I've just received a pair of Illumina FASTQ files from the sequencing facility and intend to map them to the hg19 reference genome. I first used the FASTQ Groomer utility to convert the reads into Sanger reads. However, when running Bowtie for Illumina on the resulting dataset under default settings, I received the following error:

An error occurred running this job: Error aligning sequence. requested number of bytes is more than a Python string can hold

Can someone help point out my mistake? My history is accessible at http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch

Appreciate the help!

Weng Khong, LIM
Department of Genetics
University of Cambridge
E-mail: wkl24@cam.ac.uk 
Tel: +447503225832

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Dan Webster
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