Devon Ryan

The tool is deprecated only because modern data rarely suffers from any major GC bias. Otherwise it should work fine. Sent from my iPhone > On 20. Feb 2020, at...

I wonder if this is a matplotlib bug. Can you post the gzipped matrix?

Perhaps the IO on your system is extremely slow or you have a very large number of small contigs? Those are the most common causes of poor performance.

Run `samtools view -H` on the BAM file and count the number of lines starting with @SQ. That's the number of contigs in your genome. If it's a high number...

I haven't a clue why things are so slow on your system.

You've identified where to put it, it is the scale factor. Also use `--scaleFactorsMethod None` since I don't recall if setting the scaling factors disables the automatic computation (I don't...

You'll want a bigWig file for the entire genome. See `bamCoverage` for an example of how to make a bigWig file.

That's a 3 base long region, so you're going to have issues with it. Did you artificially truncate it? You likely want `reference-point` instead of `scale-regions` if so.

That looks reasonable, though you're only clustering by a single sample then (I imagine you'd want all of the samples together when running computeMatrix). In that case you might take...

The last bin processed should never be larger than the bin size. However, the reported bins will be merged together if they have the same value. I suspect that that's...