Brett Chapman
Brett Chapman
Hi I'm using vg tools v1.50.1 "Monopoli" I've produced a graph from 7 different genomes of the same species using minigraph-cactus. I've used the indexes produced from minigraph-cactus with ```--giraffe``...
Hi I have a pangenome graph with 5 genomes generated from minigraph-cactus. I'm currently indexing with autoindex to use mpmap and rpvg. When aligning RNA-seq reads should I align each...
Hi I have vg v1.50.1 "Monopoli" I producing a graph from PGGB and would like to clip off dangling edges where coverage is less than 2 nodes. I'd like to...
Hi I have a genome graph from Minigraph-cactus I'm trying to create a spliced graph from along with indexes to run vg mpmap with and later rpvg. I tried running...
Hi I get an error while indexing. It appears that I require CSI indexing due to the length of my chromosomes. Is there a work around for this? Will you...
Hi Erik I noticed with Edyeet that the default -p is now 95% and the -a is now set to 0 by default. With previous versions of Edyeet I tended...
Hi Erik I have a question about the -M parameter for edyeet and wfmash. Since it produces a better overall mapping by merging the alignments of each segment, wouldn't it...
Hi Erik I've run Edyeet with 2 chromosomes of the same variety, but different assembly versions (related to the issue I posted for smoothxg: https://github.com/ekg/smoothxg/issues/2). I also ran with minimap2....
Hi Two features which I think would be really useful in sequenceTubeMap are: 1. On hover over a node or path more information is displayed i.e. all paths passing through...
Hi I thought I better create a new issue. I'm getting time out errors on all my requests from displaying all paths in my graph (to display paths in the...