Question: Troubleshooting: Problem TopHat paired data
gravatar for Jonathan.Burghofer
8 weeks ago by
Jonathan.Burghofer0 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 • 78 views
ADD COMMENTlink modified 8 weeks ago by Jennifer Hillman Jackson25k • written 8 weeks ago by Jonathan.Burghofer0
gravatar for Jennifer Hillman Jackson
8 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


It is possible that no hits were generated by Tophat

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:

These support FAQs about fastq data may also be helpful:

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:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 8 weeks ago by Jennifer Hillman Jackson25k
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