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Question: Troubleshooting: Problem TopHat paired data
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gravatar for Jonathan.Burghofer
10 weeks ago by
Jonathan.Burghofer • 0
Jonathan.Burghofer • 0 wrote:

Hey! I´m using TopHat and it works well for 3 of 4 samples. But unfortunately an error occurs while analyzing the fourth sample:

"file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False"

Please, can sombody help me out with this error?
rna-seq tophat galaxy hisat2 • 99 views
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modified 10 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 10 weeks ago by Jonathan.Burghofer • 0
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gravatar for Jennifer Hillman Jackson
10 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It is possible that no hits were generated by Tophat https://galaxyproject.org/support/tool-error/.

This can happen when:

  • the assigned datatype is a mismatch for the fastq data
  • the data is truncated (incomplete upload to Galaxy, or some problem with an upstream data transfer)
  • the wrong target genome was mapped against
  • the parameters set are too stringent for the data

This post includes advice to correct issues with fastq data from certain sources: https://biostar.usegalaxy.org/p/28718/#28779

These support FAQs about fastq data may also be helpful: https://galaxyproject.org/support/#getting-inputs-right

We would strongly recommend using HISAT2 instead of Tophat (the tool is now considered deprecated). To learn about the most current RNA-seq methods and tools, please see the Galaxy tutorials here: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 10 weeks ago by Jennifer Hillman Jackson ♦ 25k
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