Chao-Chung Kuo

icon indicating a website link https://chaochungkuo.github.io/ icon indicating an email [email protected]

icon company RWTH Uniklinik icon location Aachen, Germany icon location A computational biologist who likes to ask questions about life and pursues the truth.

Results 3 issues of Chao-Chung Kuo

THOR- Issue in regenerating report

3 comment

Below is the error message I got when I set `--report` in the command. I will also check it later. ``` Call DPs on whole genome. Computing read extension sizes...

bug

Fixing bugs for extracting Qiaseq UMI before trimming

1 comment

Detailed discussion can be seen here: https://app.slack.com/client/TE6CZUZPH/activity In short, the problem is: When I run this command for Qiaseq protocol, ``` nextflow run nf-core/smrnaseq -profile docker,qiaseq -resume \ --mirtrace_species "hsa"...

fastp trims the qiaseq adapter before UMI extract so no BC pattern is found for UMI extraction

2 comment

### Description of the bug The empty `fastq` files appears in this command: ``` umi_tools \ extract \ -I Healthy_E72a.umi_dedup.sorted.fastq.gz \ -S Healthy_E72a.umi_extract.fastq.gz \ --extract-method=regex --bc-pattern='.+(?PAACTGTAGGCACCATCAAT){s

bug