Microsatellite Instability, Whole exome sequencing
3
0
Entering edit mode
5.3 years ago
vaish01kv • 0

How can Microsatellite instability be calculated using Whole exome sequencing, when microsatellite is comprised of tandem repeats etc,. and classified under non-coding regions?

next-gen exome sequencing • 2.7k views
ADD COMMENT
2
Entering edit mode
5.3 years ago
bruce.moran ▴ 970

There was a good editorial on MSI in JCO PO a few years ago, alongside this paper which references the set of 2,359 microsatellites in or near the exome. So reason is that not all are in non-coding regions.

ADD COMMENT
0
Entering edit mode

How can MSI be calculated when there is no matched normal available?

ADD REPLY
0
Entering edit mode

How to identify microsatellite markers in exome sequencing, to calculate MSI?

ADD REPLY
1
Entering edit mode

Because microsatellites are so highly variable per individual, I think you will need matched normal to test MSI. Without matched normal you could investigate tumour mutational burden (TMB).

ADD REPLY
0
Entering edit mode

Thank you so much for the information!

ADD REPLY
1
Entering edit mode
ADD COMMENT
0
Entering edit mode

Thank you! But MSIsensor needs Matched normal for analysis. Is there any method where i can do it without normal sample?

ADD REPLY
1
Entering edit mode

It can work in tumor-only mode . You just provide the tumor bam file. msisensor msi -d microsatellites.list -t tumor.bam -o output.tumor.prefix

ADD REPLY
0
Entering edit mode

Hey Nicolas, I tried using this command and it says "please provide a valid format normal bam file!"

What should I do now? TIA

ADD REPLY
0
Entering edit mode

Could you post the exact command you used. check on the github of msisensor. Maybe contact the other : https://github.com/ding-lab/msisensor

ADD REPLY
0
Entering edit mode

Hey. The error is rectified. I had to give the whole path for the command to work. Thanks.

ADD REPLY
0
Entering edit mode

Hey Nicolas, I get the following error while running msisensor:

[bam_index_load] fail to load BAM index. msisensor: bamreader.cpp:184:bool ReadInBamReads(const char*, const string&, unsigned int, unsignedint, std::vector<split_read>&, std::string): Assertion `idx' failed. Aborted (core dumped)

How should I work further? Thanks

ADD REPLY
0
Entering edit mode

did you index your bam files before ie. samtools index alignment.bam

ADD REPLY
0
Entering edit mode

Yes I did and all the files are in the same directory as well.

ADD REPLY
0
Entering edit mode

do you have samtools in your PATH

ADD REPLY
0
Entering edit mode

Yes I do. SAM tools is installed in my path.

ADD REPLY
0
Entering edit mode
4.8 years ago

has anyone tired the latest software OSTRFPD: Multifunctional tool for genome-wide short tandem repeat analysis for DNA, transcripts and amino acid sequences with integrated primer designer link: https://github.com/vivekmathema/OSTRFPD

ADD COMMENT

Login before adding your answer.

Traffic: 2677 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6