Issue in Step6: ChIP-Seq data analysis tutorial: Formation of the Super-Structures on the Inactive X

Dear Galaxy Support,

I ran the ChIP-Seq data analysis tutorial.
I got error in Step 6: Plot the signal between samples (In attached picture).

  1. Concatenate two datasets into one dataset -Got Output
  2. SortBED -Got Output
  3. MergeBED -Got Error

I was still able to perform
4. computeMatrix (tried with output of Concatenate)
5. plotHeatmap

I have attached pictures of the steps and output pictures.
Could anybody try the tutorial and give advice on my issue?

Thanks in advance.

I have detailed the issue in the attached picture.
Tutorial Source:


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the “29. SortBed…” dataset appears to not be sorted properly; this seems to be verified by the fragment of error message I can make out:
“Error: Sorted input specified, but…”
then it lists the second entry in “29.” – whose Start is sooner than the preceding data-point (ie, not in ascending order)

Is it possible you accidentally sorted by the wrong value? The tutorial simply says “Sort the following bed,bedgraph,gff,vcf file” so it expects the default sort parameter “Sort by: chromosome, then by start position (asc)”


Hi sargentl,

True, I too cannot find what it sorted, after chrx column, Start column should be sorted in ascending.
I did default sort criterion. Couldnot figure out so far.


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Hi sargentl,

Thank you for the quick comment and your time.
I tried SortBED and MergeBED again after your comment.
Start column got Sorted in ascending order!! :stuck_out_tongue:
MergeBED worked without Error :slight_smile:

I tried yesterday several times it didnot work. Today it worked :stuck_out_tongue:

Thank you very much.