Katrin Sameith

Peak calling parameters might not be ideal

3

Dear all, We had started to discuss this topic in Slack, but I decided to raise this issue so the comments won't get lost. In brief, you currently use the...

Genome annotation (gene names) missing in IGV session file

1

Hi there, We noticed that it would be very useful to have the genome annotation already loaded to the IGV session file that is generated by the pipeline. At the...

Mini-issues in the reporting

1

Hello there, As usual, I am so glad I can run your pipeline for our clients! :-) This time around, I found some irregularities in the MultiQC report, and just...

Pseudotime analysis

3

It would be great to extend the workflow with pseudotime analysis. Several customers would like to see this kind of analysis, see velocity or trajectory inference.

Update: Todo: - Update how to run the workflows from command line, and check all arguments Done: - Improve README - Add Singularity Recipe

Documentation of code

1

We need to go through our R/ scripts and update documentation of the functions.

Make sure a new analysis writes into an empty results folder

1

I regularly face the issue that I re-run an analysis, and overwrite old files. Sometimes by mistake. Sometimes on purpose, but then there are often still old files remaining, e.g....

How to automatically use your style.css

2

Dear Felix, Thank you for providing this repository! For our bioinformatics work at the DRESDEN-concept Genome Center, we started to write Markdown files to provide READMEs to our collaborators. We...

The correction of ONE insertion leads to MANY base changes, because all bases following the insertion are shifted. Reported metrics represent base changes, not base corrections. Thank you for providing...