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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ? #9

Open PengJia6 opened 4 years ago

PengJia6 commented 4 years ago

Add scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ?

zhufengjao commented 3 years ago

Add scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ?

Hi Pengjia, Recently I have install MSIsenor-pro and run the tumor_normal.sh for test，then I got the MSI score 9.58% (Number_of_Somatic_Sites %) .Now, How to classify the MSI high and MSI low ? Looking forward to your reply. Thanks.

PengJia6 commented 3 years ago

Add scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ?

Hi Pengjia, Recently I have install MSIsenor-pro and run the tumor_normal.sh for test，then I got the MSI score 9.58% (Number_of_Somatic_Sites %) .Now, How to classify the MSI high and MSI low ? Looking forward to your reply. Thanks.

Sorry！ I will finish it in the following week. Please tell me your email address and I will contact you when I finish it!

zhufengjao commented 3 years ago

Add scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ?

Hi Pengjia, Recently I have install MSIsenor-pro and run the tumor_normal.sh for test，then I got the MSI score 9.58% (Number_of_Somatic_Sites %) .Now, How to classify the MSI high and MSI low ? Looking forward to your reply. Thanks.

Sorry！ I will finish it in the following week. Please tell me your email address and I will contact you when I finish it! My email is fengjiaozhu9@163.com. Thank you very much.

PengJia6 commented 3 years ago

Add scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ?

Hi Pengjia, Recently I have install MSIsenor-pro and run the tumor_normal.sh for test，then I got the MSI score 9.58% (Number_of_Somatic_Sites %) .Now, How to classify the MSI high and MSI low ? Looking forward to your reply. Thanks.

Sorry！ I will finish it in the following week. Please tell me your email address and I will contact you when I finish it! My email is fengjiaozhu9@163.com. Thank you very much.

How many samples do you have? And what sequencing technology did you use? WGS? WES? or target gene sequencing?

Alviner-Heo commented 2 years ago

Hi Pengjia, Recently I used Msisensor-pro to analyze my RNA-seq data. Msisensor-pro worked fine and got good results. However, I do not know which values to use when checking the MSI status (e.g. MSI-H, MSI-L) from the produced data. Is there a criteria to check the MSI status from the produced data? I have 290 RNA-seq samples. (Tumor 205 / Normal 85) Thanks.

PengJia6 commented 2 years ago

Hi, sorry for late reply. MSIsensor-pro is not recommended for MSI detection with RNA-seq data now.

But, we have developed a new software named MSIsensor-RNA for RNA expression data. You can try it, it does not need a cufoff.

h170607 commented 9 months ago

Add scripts for user to determine the cuf-off of MSI-H and MSS/MSI-L ?

Why not upload the scripts on GitHub as a complement to msisensor-pro?