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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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*msi_somatic file description #22

Open wyy1234-github opened 2 years ago

wyy1234-github commented 2 years ago

Hi, Thank you for developing msisensor2, it's really helpful. I am using this tool in tumor-control model, but i am not clear about the meanning of last three column of the *msi_somatic file, for example,

chr9 139390944 CGGCT 5 GTG GCGGC 0.019759 0.031458 0.044226

I look forward to your reply.

Beifang commented 2 years ago

Thank you for your msisensor2 comments.

chromosome location left_flank repeat_times repeat_unit_bases right_flank difference P_value FDR rank chr9 139390944 CGGCT 5 GTG GCGGC 0.019759 0.031458 0.044226

0.031458： reads distribution difference of Normal and Tumor 0.019759： chi square test p value 0.044226: FDR adjusted p-value ( or q-value )

For more information, please refer to the msisensor paper ( https://pubmed.ncbi.nlm.nih.gov/24371154/) or https://github.com/niu-lab/msisensor .

wyy1234-github commented 2 years ago

thank you very much. I have another question, I want to use the 7 PCR golden standard markers in tumor-control model. can you tell me how to calculate repeat_unit_binary, left_flank_binary, right_flank_binary?

Beifang commented 2 years ago

image

wyy1234-github commented 2 years ago

thank you. But I am not sure how to calculate repeat_unit_binary, left_flank_binary, right_flank_binary.

Beifang commented 2 years ago

A:00; C:01;G:10;T:11. TCGA=11011000.

bounlu commented 8 months ago

image

How about these 7 biomarkers? How to prepare the input for msisensor2 for these genes?

https://www.biocartis.com/en/meet-idylla/idylla-oncology-tests/idylla-msi-test