MSI score greater than 1

[shanshenbing]

I ran MSIsensor-pro with paired samples successfully and I found some sample has a MSI score great than 1. Actually, the MSI score is the percent of somatic sites, which can not be 1 or great than 1. So, I am confused with the result. I hope you can give me some suggestions.

[PengJia6]

I ran MSIsensor-pro with paired samples successfully and I found some sample has a MSI score great than 1. Actually, the MSI score is the percent of somatic sites, which can not be 1 or great than 1. So, I am confused with the result. I hope you can give me some suggestions.

Could you please send your command and output to me. My email is [email protected]

Thanks !

[shanshenbing]

Sorry，It‘s my fault. I didn't notice that MSIsensor-pro output is in percent and my data is just greater than 1%. And I also run msisensor with my data and I found the MSI scores of the same sample are different. Is this normal?

[PengJia6]

Sorry，It‘s my fault. I didn't notice that MSIsensor-pro output is in percent and my data is just greater than 1%. And I also run msisensor with my data and I found the MSI scores of the same sample are different. Is this normal?

This is normal, but I don't think it matters. This may caused by the different default parameters between these two programs.

[shanshenbing]

Thank you for your reply. The reason why I noticed the problem is that the difference is a little big.&nbsp; I ran msisensor-pro scan with fasta file and using the generated file for next step.&nbsp; The softwares werw run as follow: nohup msisensor-pro msi -z 1&nbsp; -b 3 -0 1 -y 1&nbsp; &nbsp; -d /path_to/Homo_sapiens.GRCh37.75.format.list \ &nbsp; &nbsp; -t /path_to/${tumor}.reorder.sort.add.mkdup.BQSR.bam \ &nbsp; &nbsp; -n /path_to/${normal}.reorder.sort.add.mkdup.BQSR.bam&nbsp; \ &nbsp; &nbsp; -o ${WORK_DIR}/result/${sample}/${sample}&nbsp; &amp; nohup msisensor msi -z 1&nbsp; -b 3&nbsp; -y 1&nbsp; &nbsp; -d /path_to/Homo_sapiens.GRCh37.75.format.list \ &nbsp; &nbsp; -t /path_to/${tumor}.reorder.sort.add.mkdup.BQSR.bam \ &nbsp; &nbsp; -n /path_to/${normal}.reorder.sort.add.mkdup.BQSR.bam&nbsp; \ &nbsp; &nbsp; -o ${WORK_DIR}/result/${sample}/${sample} &amp; note: I used the same list file generated by msisensor-pro scan. The result of first 35 samples is in the accessory, and I found the Pearson r is about 0.7 compulated with all my data.&nbsp; The parameters are similar to each other, but results are different. And I also found a relate issue at&nbsp;ding-lab/msisensor#3.&nbsp; I hope to get your advice. ------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "xjtu-omics/msisensor-pro" <[email protected]&gt;; 发送时间:&nbsp;2020年8月11日(星期二) 晚上10:24 收件人:&nbsp;"xjtu-omics/msisensor-pro"<[email protected]&gt;; 抄送:&nbsp;"单申兵"<[email protected]&gt;;"Author"<[email protected]&gt;; 主题:&nbsp;Re: [xjtu-omics/msisensor-pro] MSI score greater than 1 (#11) This is normal, but I don't think it matters. This may caused by the different default parameters between these two program. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[PengJia6]

The result of first 35 samples is in the accessory, and I found the Pearson r is about 0.7 compulated with all my data.  The parameters are similar to each other, but results are different. And I also found a relate issue at ding-lab/msisensor#3. 

The msi module in msisensor-pro is inherited from msisensor, the results should be same. Could you please add -c option to the two command and try again, because there is a small bug in the default parameter, please see #8 .
Please let me know if this is workable and feel free to contact me if you have any question.

[shanshenbing]

I wrote the last comment in QQ mailbox and the space character was converted into '  '. I am sorry for the confusing meaning. I checked msisensor default parameters and found the default -c in msisensor is 20, so msisensor-pro was run with -c 20. The result of the two software are same. Thank you for your help! Maybe the next release of msisensor-pro can change the default value of -c parameter.

[PengJia6]

@shanshenbing Thanks, I had updated source code and binary version, and conda version would be updated later. Thanks for using our software and give feedback, if you have other questions, please open a new issue or contact with me directly.