Lijia Yu

Hi @gtca , Problem solved, i forget to install cupy... so the correct packages in env should includes: ``` _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge anndata 0.9.2 pypi_0...

Hi @jo-mc , Thank you for your quick response. it is sorted bam file. Is it possible that the string 'HLA-DRB1\*16:02:01' including the asterisk (*), could cause an error when...

Hi @jo-mc , Thanks for your suggestion. My bam file header includes all chromosome name in the fasta file, one HD line and two PG lines. I am not sure...

Hi @jo-mc , Thank you for doing a lot of tests! Based on your testing, it seems that the sequence of ALT, decoy and HLA genes makes it challenging for...

Hi @jo-mc , I remapped my data with GCA_000001405.15_GRCh38_no_alt_analysis_set.fna. However, in the first step, I encounter the Segmentation fault error every time. I use the adapter tag to prevent the...

Thanks! The BAM file I used above has undergone read recalibration with GATK. However, ReSeq cannot process data with recalibrated reads. Fortunately, I can run ReSeq successfully using directly mapped...

Hi, Would you mind providing a reproducible example? I think Highcharter is one of HTML widgets that creates interactively data visualisation. I feel it is difficult to create gifs based...

you dont need to build this theme. just try `jekyll serve ./` in the theme folder.

Hi, You could use `cnvkit.py access` command to generate any sequence-accessible coordinates file by yourself. Please see this page https://cnvkit.readthedocs.io/en/stable/pipeline.html#access Calculate the sequence-accessible coordinates in chromosomes from the given reference...

@stroke1989 @awast Please see this post to find the the mappability file https://www.biostars.org/p/487547/