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.cufflinks@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.
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