Brett Chapman
Brett Chapman
Hi I'm trying to load my GFA file, but I'm getting an error. ``` gfaestus *.smooth.gfa *.smooth.chop.og.lay loading GFA loading GFA with 734 nodes, 1003 edges adding nodes adding edges...
Hi While running vg autoindex I get complaints about the sequence length being too long. I had the same problem when running vg gbwt, so I set the buffer size...
Hi I'm running vg version 1.34. I'm attempting to create a splice graph. I have a GTF file where the first column represents the paths in the graph across all...
Hi I've been getting the following error when working with plant genomes. I've also flagged the error with bx-python (https://github.com/bxlab/bx-python/issues/67): ``` inner_distance.py \ -i Root_1.markdup.sorted.bam \ -r RGT_Planet.bed \ -o...
Hi I've recently come across a forum (https://www.biostars.org/p/89088/) which mentions that bwa mem should be run with Phred+33 Illumina reads instead of Phred+64. My Illumina library is Phred+64, and I...
Hi I've been getting a segmentation fault when running speedseq sv. The problem appears to stem from Lumpy. I've tried with a dev version of Lumpy and I still get...
Hi I've just been going over the demo visualisation and noticed that the links within the Linear View: Annotations section has links to genes/repeats under the "Name" column which do...
Hi This is an amazing genome graph visualisation tool you have developed. I'm currently trying to get it to run. I can run locally on my laptop with the demo...
Hi I'm really interested in using your pipeline for TE analysis of multiple different non-model organisms. I'd prefer to use your tool through Docker on the command line to speed...
Hi I'm interested in producing dendrograms, heatmaps, network plots (force directed network plots) and hierarchical edge bundle plots using the final merged members of each module. From what I've read,...