4 months ago by
Ok, that went quicker than expected. The skipped BED transcripts are not represented in the bigWig file. This might be Ok depending on your analysis goals.
An example input region that was skipped because it hit to an unmapped chromosome not included in the BAM/bigWig:
chrUn_GL456372 6883 13335 uc009skg.1 0 - 6883 6883 0 3 680,151,109, 0,933,6343,
Two choices: Use the data as is (leave out the transcripts that didn't pass through the tool). Or, recreate the BAM used to generate the bigWig using the full mm10 genome build.
I only see a small number of skipped transcripts/regions (for this reason) when I review the
stderr for the job. Click on the job details icon ("i" icon) to review this content. You can also send in a bug report - I'll know it is yours, so is fine to do that without expecting more feedback - and you'll get a copy to self-review the full details.
Overall, 63,814 regions were input and 63,572 matrix lines were generated. The difference of a few hundred are most likely those transcripts that were not in the bigWig at all (skipped).
The current results appear to be Ok to plot. If you have a have a failed plot (I couldn't find one active in your history), a bug report for that can also be sent in/reviewed for more details about why that is failing. It could be that some setting for ComputeMatrix needs to be tuned. For example, you might want to set the parameter "Skip zeros" to "Yes" (what this exactly does is explained on the tool form). In short, when no overlap is found for the transcript regions vs any of the bigWig's regions those data will be removed from the heatmap plot output.
Hope that helps! Jen, Galaxy team