Albert Vilella

One could limit it to input bed file of non-overlapping regions, which would make the 5primemost and 3primemost possibly easier to implement. Maybe not... Thanks a lot for all the...

Or is it a matter of flipping around the bed regions so it clips outside the regions?

Apologies, I wrongly wrote t-test in the description but then copied the fisher.test line of code. Corrected now.

Yes, as far as I can tell this is the way people can contribute to the visualizations. I have to say that my JS skills are next to zero, so...

Not sure if there is a micropayments method to encourage tickets in this repo @jameswex . Anything that can be done? Also, I believe there is now an open call...

The only issue I could see are the downloading of the of fonts, but the page looks fine on Firefox 99.0.1 (64-bit) Windows 

Here is an example file where the image above comes from: https://dl.dnanex.us/F/D/bygGZ2v3Y8qq8Pp8YGFyKyp81bp4xbJ67Bzk618X/CEG60-53-C1-oxBS_S1_L001_R1_001.1.cutB.seqtk_revcom.u.bwameth.paired.primary.barcoded.2Df.sorted.bam https://dl.dnanex.us/F/D/kB19gVB0qjpP236Jzv9KjxBgjk7g7XgB0PqqQkPv/CEG60-53-C1-oxBS_S1_L001_R1_001.1.cutB.seqtk_revcom.u.bwameth.paired.primary.barcoded.2Df.sorted.bam.bai It's small in size but has high coverage concentrated in certain regions.

The reference is the standard GRCh38Decoy from NCBI: https://dl.dnanex.us/F/D/jzGpFXgf85p8XQB3JVYY9fxYkFXVgQqP062Jx8v4/Homo_sapiens_NCBI_GRCh38Decoy.genome.fa The reads where aligned with bwa-meth: > python bwa-meth/bwameth.py --threads 36 --reference include_indexes_dir/input/GRCh38Decoy.fa CEG60-53-C1-oxBS_S1_L001_R1_001.1.cutB.seqtk_revcom.u.fq.gz CEG60-53-C1-oxBS_S1_L001_R1_001.2.cutB.seqtk_revcom.u.fq.gz --prefix CEG60-53-C1-oxBS_S1_L001_R1_001.1.cutB.seqtk_revcom.u.bwameth

Let me know if I can supply any more relevant details...

Thanks, I can give it a try when there is a `bwameth --pbat` to try. On Thu, Aug 10, 2017 at 3:34 PM, Devon Ryan wrote: > A small update,...