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Question: Inputs not recognized by tool
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gravatar for puneetd
4 months ago by
puneetd • 0
puneetd • 0 wrote:

I have uploaded two bam files to Galaxy to generate HTSeq counts. However, both my bam file and genome gff file are not being recognized in HTSeq. Can you help me figure out what's wrong?

Thanks Puneet
database metadata galaxy datatype input • 120 views
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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by puneetd • 0
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gravatar for Jennifer Hillman Jackson
4 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You probably need to assign the datatype and/or database to the inputs.

Also, be sure to double check the GFF/GTF format - this tool has specific content/format requirements described on the tool form - please be aware that the tool does not accept GFF3 formatted annotation. The attributes gene_id and transcript_id must be present in the 9th field. If a custom genome/build is used, that must also be formatted correctly.

FAQs that will help with the above: https://galaxyproject.org/support/#troubleshooting.

Start with these:

  • The tool I'm using does not recognize any input datasets. Why?
  • How do I find, adjust, and/or correct metadata?
  • Common datatypes explained
  • Preparing and using a Custom Reference Genome or Build
  • Mismatched Chromosome identifiers (and how to avoid them)

If the job later fails, there is likely an input format/content problem. This FAQ has summaries that link to other more specific FAQ help, including those listed above:

  • My job ended with an error. What can I do?

Galaxy Tutorials covering tool/workflow usage help within a scientific context:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k
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