Olga

Thank you, lh3 for your advice to use minimap2, I will do it. But just for curiosity, I would like to know the mathematical approach for 'bwa mem". And can...

### Hello. **I am running HiC-Pro on a cluster through:** ./bin/HiC-Pro -i rawdata -o hic_results -c config-hicpro.txt -p I got this error: The following command will launch the parallel workflow...

Hello, I try to run a HiC-Pro as well and I got this HiC-Pro_3.1.0/bin/../scripts//Makefile:181: hic_qc] Error 1  And in plot_mapping_portion.Rout i have this. > #################################### > ## > ##...

Hello! I have an issue to proceed with the data analysis after Pore-C-Snakemake. I don't see the .bedpe output file Could you, please, guide me or show me if I...

Hello. I got a bunch of bam files from the pipeline. I merged them all together with samtools merge all.bam *.coord_sort.bam and to proceed with the analysis I have to...

Thank you for this amazing pipeline. It's a really powerful tool for data analysis. I would like to ask about the meaning of each parameter in the alignment part. Could...

Hello! Could you please help me with the following issue: When I run the Snakemake pipeline it give me an error: "rule bwa_index_refgenome: input: results/refgenome/Tb.rg.fa output: results/refgenome/Tb.rg.fa.bwt log: results/logs/results/refgenome/Tb.rg.fa.bwt.log jobid:...

I create and activate the env: 1. [name@beluga2 ~]$ virtualenv venv_pore_c && source venv_pore_c/bin/activate 2. [name@beluga2 ~]$ pip install --no-index --upgrade pip 3. [name@beluga2 ~]$ pip install --no-index pore_c After...

Hello! I am trying to run the Pore-C-Snakemake pipeline. But I don't understand how I can modify the "phased_vcfs.tsv" file in **config** folder to complete all modifications before running the...

I have never run those kind of pipelines from PC not from cluster. Could you please help me to run it? What I have to install to be able to...