Dexin

coverageBed killed

1

When I ran this command, coverageBed -counts -a a.bed -b b.sort.bam > c.tsv, the process broke down. The b.sort.bam was around 2.3G. coverageBed: line 2: 137437 Killed ${0%/*}/bedtools coverage "$@"

Hi, After performing bwa mem to align reads to the reference genome, I am wondering whether I should filter the low-quality mapped reads (e.g., samtools view -q 30)?

Whether I can use single nuclei RNA-seq data as input

1

I am wondering whether I can use single nuclei RNA-seq data as input. Compared with scRNA-seq, snRNA-seq tends to capture the mRNA inside the nuclei. I think this might introduce...

Modification calling missing for the inter-chromosomal translocated reads

8

Hi, First, I appreciate your wonderful tools for analyzing nanopore data. Recently, I have been trying to use **Dorado 0.7.0 v5.0.0 HAC** to call the base and modification from pod5...

Indel calling for illumina WGS

2

Hi, Thanks for developing such an amazing tool. I am wondering whether ClairS supports the indel calling for Illumina WGS. Thanks, Dexin

Clarification on --model parameter in modkit open-chromatin predict

1

Hi, Thank you for developing such a powerful and user-friendly tool! I’m currently working on open chromatin prediction using modkit and had a question regarding the `--model` parameter in the...

6mA modification missing after modkit callmod

3

Hi, The top track is the raw BAM file (grouped by read strand) after dorado base&modification calling. After I used the default` modkit call-mods ` (bottom), I found some of...

Copy number alteration correction

2

Hi, Thank you for developing such an amazing tool. When analyzing some cancer cell lines (e.g., K562 and HepG2), I was wondering whether copy number alterations (e.g., whole-chromosome gains or...