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Question: Problem with HISAT
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gravatar for rr14049
2.1 years ago by
rr14049 • 0
United Kingdom
rr14049 • 0 wrote:

Hi,

Im trying to run a custom workflow for RNA-seq data structured as follows:

  1. Inputs: reference genome (GRCm38), forward and reverse (paired-end reads)

  2. these feed into HISAT and the outputs of this into Cuffdiff along with GRCm38.85 gtf file.

Unfortunately I keep getting the following error message:

Fatal error: Matched on error [22:18:01] Loading reference annotation and sequence. No fasta index found for /galaxy-repl/main/files/017/273/dataset_17273202.dat. Rebuilding, please wait.. Fasta index rebuilt. Warning: No conditions are replicated, switc

Please does anybody have any ideas about what the problem could be here? Any help would be much appreciated! Many thanks.
rna-seq hisat cuffdiff • 763 views
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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by rr14049 • 0
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gravatar for Jennifer Hillman Jackson
2.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is at http://usegalaxy.org?

It appears that something is wrong with either the inputs or parameters. Double check all inputs to make sure from the same exact reference genome. The library type warning is usually not a fatal error - the default type will assign automatically, but you can also have a look at params set vs the manual. https://wiki.galaxyproject.org/Support#Reference_genomes

Best, Jen, Galaxy team
ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
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