limin

icon company @UCDavis icon location Working on Genetics, Genomics, Bioinformatics, and both NGS and Third generation sequencing data.

Results 15 issues of limin

unicycler hybrid assembly generating loops?? why???

Hi I have both illumina pair-ends short reads of 300 bp, and nanopore long reads for my bacteria. Now I am using unicycler for hybrid assembly. I then use bandage...

Fail to run TestSet using panX

11 comment

Hello I am teaching myself how to run panX using TestSet. Here is the command I run exactly following the instructions. ./panX.py -fn data/TestSet/ -sl TestSet -t 32 > TestSet.log...

each input fasta file has more than one chromosome and plasmid?

I have dozens of bacterial genome with high assembled quality, and each genome has 2 chromosome and two or more plasmids. since parSNP only align core genes and call SNPs...

Fail to start the image

When I tried to start the image on my mac, I ran into the following errors. Any suggestions on how to troubleshoot it? Best, LC

cnvkit import-rna AssertionError: gene_id

I am running cnvkit.py import-rna, and it gave me the following error: the cnvkit version is 0.9.9. ``` (cnvkit) limin@DERM-6NBQ05N-LT cnr % cnvkit.py import-rna -f counts -g /Users/limin/miniconda3/envs/cnvkit/data/ensembl-gene-info.hg38.tsv -c /Users/limin/miniconda3/envs/cnvkit/data/tcga-skcm.cnv-expr-corr.tsv...