Hello,
There is a bug in Bowtie right now. We have the fix for this ready, but
it won't be available until the main server is updated and restarted. In
the meantime, you can use Bowtie on our test server
(
), which has the updated code on it (just be
aware that you can't transfer history items directly from our test
server to main). I am sorry for the inconvenience.
Regards,
Kelly
On 4/6/10 4:33 PM, Dan Webster wrote:
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...
Best,
Dan
On Tue, Apr 6, 2010 at 1:20 PM, Weng Khong Lim <wengkhong(a)gmail.com
<mailto: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(a)cam.ac.uk <mailto:wkl24@cam.ac.uk>
Tel: +447503225832
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--
Dan Webster
Ph.D. Student - Cancer Biology
Laboratory of Paul Khavari
CCSR BLDG, Rm 2150
269 Campus Drive
Stanford, CA 94305
DanWebster(a)stanford.edu <mailto:DanWebster@stanford.edu>
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