Hello Suzie,
There are two considerations:
1 - Will Bowtie allow very short sequence to be used as the reference
genome? The answer appears to be yes, from the tool documentation.
http://computing.bio.cam.ac.uk/local/doc/bowtie2.html#what-isnt-bowtie-2
It is certainly worth testing. Questions about configuration or tuning
parameters for this type of case would probably best be addressed to the
tool authors at tophat.cuffli...@gmail.com.
2 - Will Galaxy permit short sequences to be used as custom reference
genome? The answer for this is also yes. A custom reference genome can
(in theory) be any nucleotide fasta file.
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Since your data is in MAF format right now, you will need to convert it
to fasta. Use the tool "Convert Formats -> MAF to FASTA".
Using Galaxy: tutorial #5: Working with Multiple Sequence Alignments
goes through many manipulations with MAF data to address cleanup,
conversion, labeling, etc.
http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
And for an overview about working with all of the MAF tools in Galaxy,
please see this publication (plus many of the tools have the figures
from this paper directly on the tool form itself):
http://main.g2.bx.psu.edu/u/dan/p/maf
Hopefully this helps!
Jen
Galaxy team
On 8/12/12 1:59 PM, Suzie Hight wrote:
Hello all,
Is there a way to use a library of shRNA sequences as my custom genome
when using Bowtie? Currently my library is in multiple-sequence FASTA
format.
Thanks for any help!
-Suzie Hight
------------------------------------------------------------------------
UT Southwestern Medical Center
The future of medicine, today.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
