new to needed

after reading some and watching some galaxy videos. I tried to use my alignmnet bam (generated by tophat) files to check the strandedness. However i get this error message … can you please help me what could be issue.

what i did:

  1. use rseqc to import bam files and run infer_experiment
  2. run multiqc to view the result
  3. After running this multiqc i get the error which i attached in this post. please take a look
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I don’t know how to help you with this specific problem. But, if you hit that button that has a little bug on it, you can see more detail about the error. That may help you identify the cause.

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I recognize the problem now just from the bit of screenshot already posted.

An error in an expanded dataset that states: 'Fraction of reads explained by' not found in the file means that one or more of the Infer Experiment reports input to MultiQC is empty. This should be handled better – I’ll make a request. Meanwhile, you need to find out why any of the reports are empty at all (unexpected in a tutorial) and decided if that is actually expected or if some upstream tutorial step went wrong.

These “emtpy” Infer Experiment reports will be green with one line of content (a datatype warning). Results like this could be due to a few reasons that are all rooted in the same problem: no reads were counted up into the report. Meaning, no reads were present in the BAM that 1) overlapped with the regions provided and that 2) met the rest of the criteria set on the tool form.

There could be a true content issue (poor read quality, poor target genome quality, poor mapping results – or – the results filtered too aggressively). And/or there could be some usage issue, which is more likely with a tutorial. Examples: the wrong genome was mapped against, or the annotated regions are not based the same exact genome build as the reads were mapped against in the BAM, or some related data mismatch reason contributed.

This is from a tutorial, correct? Back up a few steps and check your work. It seems like something went wrong at an upstream step.

Best, Jen


Did you set the tool form for RSeQC: Infer Experiment reports?

If you want help, please reply back with:

  1. A screenshot the tool form (configured). Make sure it includes the full tool name and version at the top. Tip: Click on the “rerun” double-arrow icon (for either of the error datasets) to bring the original tool form with the original settings back up into the center panel.
  2. If you are working on a public Galaxy server, it may help to know which one. Share back the baseline URL (copy/paste) or a screenshot of that part of the browser window, too.
  3. Or, if you are running Galaxy another way, please explain a bit more about the situation.

We can start troubleshooting from there! Thanks