Devon Ryan

It should be covered, can you provide a BAM file and the command that's producing this behavior?

That might be beneficial in this case. We don't have a way to do that built in, perhaps there's something in wiggletools that can filter a bigWig file?

I would generally use `--referencePoint start` for that use-case.

BigWig formats stores floating point values, not integers, so even without normalization values like 1 or 2 will still get stored as 1.0 and 2.0. The size of the fasta...

The most likely cause is that you have no proper pairs. Improper pairs are filtered out, since there's no coherent way to shift the resulting fragments.

Is your data extremely sparse?

That's quite sparse, you're not going to end up with a nice heatmap of BS-seq data.

I'm looking into this now.

This is a misunderstanding that may be cleared up by looking at the underlying code: ``` start = b.pos end = start + b.query_alignment_end if b.is_reverse and not b.is_read2: end...

That seems quite odd, I'll have to see if I can reproduce this. Can you post the BAM files somewhere? That will help me in tracking this down.