Entering edit mode
4.1 years ago
sruthi ▴ 40
Hi community. There is another tool "VisualMSI" for MSI calculation and its installation steps are here When I run the command:
visualmsi -i tumor.sorted.bam -r hg19.fasta -t targets/msi.tsv
it says visualmsi command not found.Could anyone tell me how to troubleshoot it?
Hey Ranan, Thanks will do it. I had saved binary earlier.
If you have saved then binary then do this:
Suppose you saved the binary in "Download" (~/Home/Downloads) Folder using wget http://opengene.org/VisualMSI/visualmsi
Go to Downloads and provide: sudo chmod 777 visualmsi
sudo cp visualmsi /usr/local/bin
Then Execute from anywhere.
Can bed file be given instead of tsv?
Please go through the Target file generation: BED convert to tsv.
Okay. Thanks will check it out. The tsv file given in the target folder is based on hg19 coordination, what must I do to get a target file based on hg38 coordination? Is it enough to convert hg38.bed to tsv?
It is always better to use one version. Either hg19 or GRCh38. If you have hg38 then convert it to hg19 coordination system.
Agreed. But I have been using hg38 for all my analysis, hence. Now, how do I convert hg19 coordination to hg38?
And when the value is 0 for "entropy of tumor data", "supporting reads of tumor data" and "quality control:failed", does it mean, the sample is MSS/ No microsatellites or is something wrong?
and yes ... you have to convert hg19 to hg38.
Something wrong. It should not be like that.
Try Using other tool:
Thanks Ratan. I have read about all the tools and most of them need matched normal except mSINGS, MSIsensor. For msiNGS: I need to create baseline file with 10-20 normal samples, which I do not have access to. In MSIsensor: I'm getting 0 even after setting -c to maximum and minimum numbers.
Coming back to conversion of hg19 to hg38. What tool should I use for conversion. Tools in UCSC?
Another doubt, I have bed file for hg38. How do I convert it to tsv? I do not understand the conversion steps mentioned here
Could you please explain it to me? TIA
It is already well explained in the file.
Hi, README.md file clearly says "higher the EMD, more chances of MSI locus to be instable", and EMD is evaluated against a normal sample. Then how does the algorithm work for case-only mode?
Could anyone just explain this? TIA