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Question: Error with Bowtie2 mapping against rhesus monkey reference genome
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gravatar for pfaller.christian
15 months ago by
pfaller.christian • 0
United States
pfaller.christian • 0 wrote:

Hello! I am trying to align a fastq file (fastqsanger) with Bowtie2 against the built-in reference genome for Rhesus monkeys (rheMac2, rheMac3). With any of the available reference genomes I receive the following error:

Could not locate a Bowtie index corresponding to basename "/galaxy/data/rheMac3/bowtie2_index/rheMac3,/cvmfs/data.galaxyproject.org/managed/bowtie2_index/rheMac3/rheMac3" Error: Encountered internal Bowtie 2 exception (#1) Command: /galaxy/main/deps/_con

Does anybody have an idea what the problem could be? Thanks! Christian
rhemac known-issue bowtie2 index • 411 views
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modified 15 months ago • written 15 months ago by pfaller.christian • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

These genomes are known to have issues with certain tools at http://usegalaxy.org and at the rsync server that hosts indexes for local Galaxy use. We plan to fix these issues in the near term. Progress can be followed here: https://galaxyproject.org/support/data-issues/

Meanwhile, a custom genome could be used instead. Or a personal local, docker, or cloud Galaxy could be set up with the indexes created directly using Data Managers. Or an alternate public Galaxy used (you'll need to check which have the tools/data needed).

Thanks for reporting the problem, Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for pfaller.christian
15 months ago by
pfaller.christian • 0
United States
pfaller.christian • 0 wrote:

Thank you for your help, Jen!
ADD COMMENT • link written 15 months ago by pfaller.christian • 0
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