zyh4482

I have some concatenated fq for quality control. When I check the report, I found something unexplained. The GC/AT base content line crossed at around 90 bp.  After using...

Failed to run the VEP annotator

4

I have 77 vcfs, of which 73 are successfully converted to maf using vcf2maf.pl. The remaining 4 files reported `ERROR:Failed to run the VEP annotator` Here is the log of...

split-vep CSQ extraction

5

I would like to present a test report for this plugin because I found that someone else met the same issue before, but with few clear answer. The purpose of...

When I tried to use MMSplice plugin, it comes with error message: ``` running code: vep -i ~/data/in.vcf.gz --vcf --no_stats -o ~/data/out.vcf --cache --plugin MMSplice ``` ``` 2022-04-12 17:44:48.311714: W...

Spladder test stuck

2

Following is my computer setup. CPU: i7-11700. RAM: 102GB I have around 200 tumor and 100 normal bams. I tried with the following command: `spladder test --conditionA tumor.txt --conditionB normal.txt...

example model

2

Hi, May I ask the model under your model path is already trained with full size of a certain TCGA cancer cohort or not? Can I use it as the...

Input file

1

Hi. I'm new in molecular dynamics. May I ask several silly questions? 1. How to generate the input file with MDtraj format like .xct and .gro? 2. If the target...

Save space at merge step

6

Hello! I'm working on large cohort with thousands of samples ( > 100 TB). However, due to the limitation of storage, it is not possible to keep all aligned reads...

The output from proteinToGenome has empty value

1

As an example, I would like to map the 1-28 amino acid of `ENSP00000518892` back to its genomic coordinates. According to `biomaRt` query result, the respective transcript sequence should be:...

I used copilot chat. Everytime I asked a question, it will always return python code in RStudio...I need to specify `use R code` in the chat block. Is there a...