Floris Barthel
Floris Barthel
I am conducting a miso analysis for a single gene on a large number of RNAseq bams that is spread out on several external HDs (twenty 4tb drives). Computing insert...
I have recently started getting the following "warnings" (suppressed when checking ignore import errors) when importing my database, but I have no idea what causes them. ``` [3] src/resultset.cpp (131)...
One of the really nice features of `vcf2vcf` is the genotyping feature. I don't know any other software that really has this capability. I've tried using `freebayes` force-calling which is...
Hi there! Thanks for the great phangorn package. I'm having some trouble using this with binary data and wonder why this is. I have two issues: 1. Using my data...
Hi, I have found several examples where a deletion (or duplication) is detected within a region that has already been deleted according to another event. For example, take (1) and...
Hi! I'm trying to understand the difference between ++ and -- strandedness in BND's with both break-ends on the same chromosome. From [here](https://github.com/hall-lab/svtools/issues/104) I understand that these are one-sided inversions....
In a test sample I'm finding that `selectSolution` is not selecting "what should biologically speaking" be the best solution. For some reason, it prefers this ploidy=4, clusters=3 solution: ``` Normal...
Hi @gavinha, This seems to make sense to me, but not sure if this was done before and/or makes sense to you. But could one get the cancer cell fraction...
Hi! I'm wondering how to use the new GATK4 copy number segmentation as input to TITAN. I guess it should be possible (see eg. https://software.broadinstitute.org/gatk/documentation/article?id=11088) but I'm not sure how....
I am trying to use Xenome to filter xenograft mouse reads from graft human reads. I am running into the issue that xenome classify finishes in seconds and returns kilobyte...