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Question: Mapping Reads To An Shrna Library?
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gravatar for Suzie Hight
6.3 years ago by
Suzie Hight • 30
Suzie Hight • 30 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.
alignment bowtie • 1.0k views
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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Suzie Hight • 30
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gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
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