Python error when running Bowtie for Illumina
by Weng Khong Lim
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
Tel: +447503225832
12 years
search in libraries
by Davide Cittaro
Hi all,
how does the library search tool work? I'm trying on the public galaxy but I can't get any result...
d
/*
Davide Cittaro
Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy
tel.: +39(02)574303007
e-mail: davide.cittaro(a)ifom-ieo-campus.it
*/
12 years, 5 months
Rhesus Macaque genome in lastz
by Lakshmanan Iyer
Hi
In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque
genome.
The web site says:
"If your genome of interest is not listed, contact the Galaxy team"
Could you please make this reference genome available?
Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly
-best
-Lax
12 years, 6 months
hesus RheMac2 genome
by Lakshmanan Iyer
Hi
In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque
genome.
The web site says:
"If your genome of interest is not listed, contact the Galaxy team"
Could you please make this reference genome available?
Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly
-best
-Lax
12 years, 7 months
Running workflows from the command line
by Erick Antezana
Hi,
I was wondering about the status of the implementation that could
support/enable running wokflows (build using the Galaxy interface)
from the command line.
cheers,
Erick
12 years, 7 months
parallelizing an NGS mapping workflow
by Chris Berthiaume
Hello,
I'd like to use Galaxy on our local beowulf cluster for NGS workflows. One typical use case we'd be replacing with Galaxy is a parallel BWA alignment of large fastq files. To distribute this across the cluster we split the fastq file into many parts, run each separately against the same reference, and then use samtools to merge the SAM output. It's not uncommon to end up with hundreds of parts after splitting. How does Galaxy handle the parallelization of large NGS mappings? I've found the tools for fastq QC, mapping, and SAM merging, but couldn't find any set of tools that would control the parallelization. This trouble ticket (http://bitbucket.org/galaxy/galaxy-central/issue/197/starting-workflows-w...) would suggest this functionality hasn't been implemented yet, but it seems necessary for many (most?) Illumina or SOLiD runs to get a reasonable mapping turnaround time. If this is already a feature it would be great if I could be pointed to the relevant docs and maybe it could be given a more prominent place in the wiki/interface. If it's not yet a feature, is there a timeline for when it will be added?
Thanks,
Chris
--
Chris Berthiaume
Center for Environmental Genomics
University of Washington
12 years, 7 months
