Tunc Morova

strand-bias settings

1

Hi, I am using strelka 2.8.0 in somatic variant calling workflow and something confused me so. version 2.9.0 configureStrelkaSomaticWorkflow.py strand bias is reporting as follows. ( this is same in...

Explanation about somatic EVS interpretation

2

Hi, I have question regarding the interpretation of somatic EVS score. Based on Strelka2 publication, it was introduced as a phred-like score. So can I take. ``` Probability of incorrect...

Hi, Thank you for the tool. My PI loves venn diagrams and it was very painful to draw them manually. I have couple minor suggestions. 1) I tried to get...

Depth first execution.

5

Snakemake versions: - 7.24.0 and 8.1.0 **Is your feature request related to a problem? Please describe.** PROBLEM: I have a pipeline with 2 rules. Download fastq and align. I want...

Performance on Xenium/Merfish(Vizgen) - Single cell integration

2

Hello, First of all thank you very much for coming up with a detailed tutorial. It made my life easy. I am trying to implement Tangram to integrate recent xenium...

Kallisto total UMI difference between velocity and novelocity modes. (single cell)

4

Hello, Thank you for keeping kallisto alive. These days, more and more I realise how its actually important and hard maintain and update tools across many years. # Background: I...

Hi, Thank you very much for the tool. I am very interested using this tool as the only label we have in the data is the dataset names (~samples). The...

How to run barcodeSwapping and ChimericReads with no h5 info?

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Hi, First of all thank you for coming up with such a critical procedure that would effect almost all single cell study. Background: We implemented 10x to our in-house method...

Inconsistent exit codes

2

Hello, Great tool. Super useful. Especially one SRX deal with all SRRs is a life saver. Many thanks. I have two scRNAseq datasets. I shared the examples below. I am...