Question: TopHat Dataset generation errors
gravatar for yasser.morsy
2.4 years ago by
yasser.morsy10 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: [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 • 752 views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson25k • written 2.4 years ago by yasser.morsy10
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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.

Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at

Thanks for using Galaxy, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson25k
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