msisensor-pro

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Hello, I have a total of more than 100 files on cancer, but there is absolutely no corresponding normal samples to use as a control, I see that I can...

20221122

RT As microsatellite sequences are repeated sequences...

Weiyifan

try to run as following msisensor-pro scan -d /local/db-build/gatk/hg38/Homo_sapiens_assembly38.fasta -o /local/scrath/test/homo.list always get errors as following failed to open file: /local/scrath/test/homo.list

songeric1107

Hi We analyzed the msi of a set of tumor-normal paired samples. The results are all above 40%, which are suspicious from experience. We used scan and msi steps. We...

h170607

Hello, I want to remove CpG context from the analysis for MSI calculation from both tumor and normal (or baseline). What is the best way to do it?

bounlu

I have compared MSI scores for the same tumor samples between: 1. its matched normal (`msi`) 2. a baseline of normals (`pro`) I had 65 tumor and 58 normal samples...

bounlu

Parallelization of samples for baseline

1

I want to create a baseline from 58 normal samples. I specified them in the config file and it runs fine with `msisensor-pro baseline` command. However, even though I specified...

bounlu

issues on toy dataset

2

Hi, When running MSIsensor-pro on a very small data for unit testing, the tool crashes saying ; ``` loading bed regions ... loading homopolymer and microsatellite sites ... Total loading...

nservant

Baseline for tumor only

5

Hello. I read you recommend at least 20 samples to make the baseline. However I don´t have that many. Can you send me the baselines file are for GRCh38 that...

da-otero

diffrent results by using diffrent homopolymer and microsates files(just diff in microsates size)

1

Hi I am running Msisensor V0.6 for some WES data. Firstly，scanning the reference file by scan model，using different size of microsates by changing parameter -s msisensor scan -l 10 -m...

ZooJooFoo