Hi @bioiz
Which tool are you using to convert the BAM to a bigWig file?
Remember that MACS2 can report “overhanging” chromosome coordinates. That means you need to use a conversion tool that has an extra option to trim those down before using certain tools.
The tutorial data is fine with the version of the tool in the hands-on, and the workflow mentioned here in the tutorial uses a version of the tool that will trim correctly.
You can also find that tool here directly:
If you open up the full parameter list, you’ll see the default option toggled on for the trimming.
In general, if you ever see a tool again complain in a message about mismatched chromosome lengths, there are three primary things to check:
- that the correct reference genome is assigned to the input metadata (database, or fasta index)
- the option of a form is set correctly – the target reference database/fasta index
- then, rarely, consider looking for minor tool quirks like I am describing here.
MACS2 is the only tool I can think of right now that reports those “overhanging” coordinates in a bed-style file but I am sure there are others! Please review this discussion at the MACS forum if you are curious.
Please give that a try and see how it works! You could also consider using that workflow as a template and running it to see what happens. You can adapt it to fit your target genome, reference data, input type, etc. Or, you can later extract a workflow from your own history once you get the process worked out.
Hope this helps! 