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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Baseline for tumor only #60

Open da-otero opened 1 year ago

da-otero commented 1 year ago

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 you mention in another posts?

Thx

ankurs103 commented 12 months ago

Hello, I am also looking for normal samples to make baseline. Is it available online ?

PengJia6 commented 11 months ago

@ankurs103 @da-otero Please download the file you need from the link below.

https://github.com/xjtu-omics/msisensor-pro/blob/master/data/GRCh38.baseline_TCGA.tsv

ankurs103 commented 11 months ago

That's not the baseline configuration file I think. That looks more like "microsatellite file". The baseline file looks like this for me (trail with 3 normal samples first) but I am getting the error "Open configure file failed, please provide valid configure file !"

My script is: sudo docker run pengjia1110/msisensor-pro msisensor-pro baseline -d reference.list -i baseline.bam.configure -o .

NA12878_A9 /data/NA12878_A9.recal.bam NA12878V500 /data/NA12878V500.recal.bam NA12878_B2 /data/NA12878_B2.recal.bam

PengJia6 commented 11 months ago

@ankurs103 I think you may need to use -v option （docker run ） to mapping your local path to the docker environment path.

ankurs103 commented 11 months ago

Hi Dr Peng Jia, Thanks a lot for your response. I am just curious to know how do you interpret the results? Let's say the the result is (as shown below), will this be MSI-H or low? What is the criteria for MSI sensor pro %?

[image: image.png]

Best regards, Ankut

ANKUR B. SHARMA Contact Details:+65-84026093 @. @.

On Wed, Jul 12, 2023 at 4:44 PM Peng Jia @.***> wrote:

@ankurs103 https://github.com/ankurs103 @da-otero https://github.com/da-otero Please download the file you need from the link below.

https://github.com/xjtu-omics/msisensor-pro/blob/master/data/GRCh38.baseline_TCGA.tsv

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