Laura Uelze
Laura Uelze
Hi, I have a problem with the computeGCBias function. I installed deeptools with `conda create -n deeptools_env -c bioconda deeptools` and I successfully ran computeGCBias for a number of datasets....
I am running the following command: `/lustre/projects/dazzler/uelze/sw/bwa-mem2-lisa/bwa-mem2 index /projects/dazzlerAssembly/asm_vpTaxBacc_BK34-6/arima/linked_assemblies/assembly_haplotig1.fasta` It seems to start of fine, but then doesnt continue after the RNK step. What could be the problem? ``` Looking...
I have a similar issue to the one described here: https://github.com/chhylp123/hifiasm/issues/442, but would like to understand it better. I run `hifiasm -l 0 -o vptaxbacc_bk34-6 --seed 123 -t 48 -f39...
Unfortunately, I am unable to install docker containers, as they our system admins have decided that Docker cannot run in the cluster we use. However, we do have Singularity. I...
I have a weird issue with ploidyplot. It was working fine before: ``` PloidyPlot -e12 -k -v -T38 -o/smudgeplot/kmerpairs /smudgeplot/FastK_Table Activating conda environment: .snakemake/conda/5e1128158bcbbb147df4df6f3dcfa370_ The input table is untrimmed and...
How can I use gfaviz for hifiasm assemblies? I have a GFA of a large assembly (12 Gbp) without paths defined as output from hifiasm. I tried running gfaviz with...
I am not sure, what is going on here. This is the first time I am trying to run hic-pro, so it might be a set-up issue? I am running:...
I followed the example 2 for hpc operations as I got an `not enough disk space error` when running fastk in single instance. I completed the commands`fastk` and `fastmerge` and...
### Description of the bug I am consistently getting a ominous java error with `-profile singularity`. I tried with different java versions openjdk 11.0.1 2018-10-16 LTS openjdk 17.0.8-internal 2023-07-18 openjdk...
Hi, I have been trying out straw to plot my hic map. I would like to get a similar image to the one I get when I load the .hic...