Question: TopHat Error Occurred with Dataset
gravatar for jhardy
3.0 years ago by
United States
jhardy0 wrote:

Hello!  I am attempting to map solid colorspace data with galaxy.  I am running the pipeline as follows:

inputs=csfasta, qual, .fa, and .gff

1. Convert solid output to fastq

2. fastq groomer

3. fastq quality converter

However, when I get to "TopHat for Illumina" (v1.4.0) I receive the following error:


An error occurred with this dataset:

Settings: Output files: "/home/galaxy/galaxy/database/tmp/tmpgUZZrt/dataset_87.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: defau

Does anyone know of a solution?



solid tophat • 828 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by jhardy0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The current Galaxy toolset does not support colorspace read analysis. 

If wrappers were developed by community contributors for tools to perform these functions, they would be a welcomed addition to the Tool Shed.

Thanks, Jen, Galaxy team


ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
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