LeilyR

Results 48 comments of LeilyR

hicMergeDomains bug: `list index out of range`

could you please provide the command line you have used

hicAggregateContacts --mode inter-chr issue

The reason is that you most likely have a very low amount of contacts between chromosomes on your matrix, so the obs/exp function underlying the --transform obs/exp returns all zero....

hicPCA and compartmentalization. Setting interaction range.

I am not sure if this about our tool or the latest comment on this issue. If you are talking about how we handle hicPCA after hicAdjustmatrix , this is...

Cannot save asymmetric matrices

Thanks for reporting it. I will have a look at it asap.

hicMergeMatrixBins changes the chr size

I believe that comes from some rounding in the last bin. I do not get how had issue downstream though. Can you elaborate a bit on that?

hicMergeMatrixBins changes the chr size

I labeled it, so we will have a deeper look at it.

Add "auto" option to --yMin and --yMax of plotHeatmap

For now you could give those numebrs all to `yMax`. It is possible to provide `yMin` and `yMax` with mutliple values

Extend nucleotides to be counted on bamCoverage "--MNase" argument.

I wonder if using `--centerReads` along with `--Offset` and `--minFragmentLength/--maxFragmentLength` would already give you your desired output.

bamCoverage bin size is variable within a file and between files

If I am not wrong its default behaviour is to merge bins of no coverage that is why you got bins of different length. To skip the those regions you...

keeping track of chr:start-end of bins when using multiBamSummary in bin mode

Try `--outRawCounts`