*msi_somatic file description

[wyy1234-github]

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]

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]

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]

[wyy1234-github]

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

[Beifang]

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

[bounlu]

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