Markus Riester
Markus Riester
Hi @lbeltrame, that would be awesome. More than happy to add it as Python code for now.
Thanks so much Luca, that's super helpful. And sorry for the delayed response. I think for now I'll take whatever you have. At some point when I need it I...
Yes, I have the centromeres. Currently as serialized RDA file in https://github.com/lima1/PureCN/tree/master/data though.
Hi Nithisha, yes, something looks wrong here. But unfortunately nothing obvious. Regarding off-target, simply load an example coverage file with --offtarget in R (PureCN::readCoverageFile). If there are no or not...
- --off-target simply fills the gaps, so all the 8056 positions should be present in both. But if you filtered the BAM for intervals, the gaps are emtpy. So try...
Sorry for the late response. I would recommend using the baits BED file, not the BED file with the targeted exons. The baits BED should be more even in width...
I'm using Rsamtools. There is a developer version with CRAM support it seems. https://github.com/Bioconductor/Rsamtools/issues/21 It probably won't work out-of-the-box, but I'm happy to accept a pull request. You can always...
Thanks Ted, will change in the next release
Beautiful related paper https://www.frontiersin.org/articles/10.3389/fonc.2019.00119/full
Apologies @hanbinlu for the way too long delay. I will look into that example in the coming days. It's been a while I worked with cell lines.