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Question: Request Reference genome in Galaxy Bowtie for Illumina?
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gravatar for sshaldipurkar1
2.5 years ago by
sshaldipurkar1 • 0
sshaldipurkar1 • 0 wrote:

How do I request a reference genome in galaxy bowtie for illumina. I need to use the Burkholderia cenocepacia H111 genome. The following link has the sequenced genome (3 chromosomes):

http://www.ncbi.nlm.nih.gov/genome/475?genome_assembly_id=229618

Under Replicon info -> RefSeq -> FASTA.
bowtie galaxy chip-seq • 753 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by sshaldipurkar1 • 0
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There will be no new genome additions for this particular tool. Requests for additions for Tophat (v2) are accepted.

However, for bacterial genomes, we recommend using the Custom Genome/Build method instead. This method works with nearly every tool at http://usegalaxy.org.

Here is how: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

Dear Jennifer, Thank you for your reply. I have been able to get the reference genome in the format ".fasta" However, the screencast explains that a .fastq or .bed should be used. May you let me know how that could be done? Waiting for your response. Kind Regards, Sayali.

ADD REPLY • link written 2.5 years ago by sshaldipurkar1 • 0

Dear Jennifer,

I have uploaded both the fasta and fastq versions of my genome of interest. I downloaded FASTA files from NCBI

ADD REPLY • link written 2.5 years ago by sshaldipurkar1 • 0
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