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Question: TopHat Dataset generation errors
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gravatar for yasser.morsy
2.6 years ago by
yasser.morsy • 10
yasser.morsy • 10 wrote:

Hello I'm trying to use TopHat in public server for alignment my RNA-seq data that generated from wheat first I uploaded fasta file of wheat genome that obtained from ensmble "Triticum_aestivum.IWGSC1+popseq.31.dna.toplevel.fa"then selected in reference genome selection genome from history but Unfortunately i had an error which is Fatal error: Tool execution failed Building a LARGE index

[2016-04-16 14:12:28] Beginning TopHat run (v2.0.14)

[2016-04-16 14:12:28] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-04-16 14:12:28] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (genome.*.bt2) Dose anyone has suggestion for solving this issue? Thanks in advance
rna-seq tophat • 822 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by yasser.morsy • 10
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, this reference genome does appear to be too large to use as a Custom genome. Wheat is on our list for potential addition to the public Main Galaxy server's indexed genomes, but is not there yet. https://github.com/galaxyproject/galaxy/issues/1470

Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at http://usegalaxy.org: https://wiki.galaxyproject.org/Support

Thanks for using Galaxy, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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