Question: Microsatellite Instability: msiSENSOR
0
gravatar for sruthi
8 weeks ago by
sruthi20
sruthi20 wrote:

Hi, I'm new to Microsatellite instability and trying to work on msiSENSOR tool. I tried uploading a bam file in msisensor using the command:

msisensor -d microsatellites.list -t tumor.bam -o output.tumor.prefix

And it says: failed to open homopolymers and microsatellites file I checked the path and it is correct. Could any one tell me what has gone wrong and how I must troubleshoot?

TIA

sequencing next-gen • 209 views
ADD COMMENTlink modified 6 weeks ago • written 8 weeks ago by sruthi20

Command:

msisensor -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix
ADD REPLYlink modified 7 weeks ago by h.mon25k • written 8 weeks ago by sruthi20

The error is rectified.

ADD REPLYlink written 8 weeks ago by sruthi20

Hi, I was calculating MSI for tumor only sample using the below command:

msisensor msi -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix

It shows:

[bam_index_load] Fail to load BAM index I checked the location of files and everything is in the same directory. Could anyone tell me where I have gone wrong and what must be done? TIA

ADD REPLYlink written 6 weeks ago by sruthi20

And it also says,

Assertion 'idx' failed Aborted core dumped.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by sruthi20

Hi all, I'm calculating MSI for tumor only sample using the below command: msisensor -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix

I have tried the command for 3 different files and getting 0 for Number of MSI sites. Is there something that I've done wrongly? TIA

ADD REPLYlink written 28 days ago by sruthi20
0
gravatar for sruthi
6 weeks ago by
sruthi20
sruthi20 wrote:

When running msisensor msi command, the following error pops up. How should I take it further.

msisensor: bamreader.cpp:184: bool ReadInBamReads(const char*, conststring&, unsigned int, unsigned int, std::vector<split_read>&, std::string): Assertion `idx' failed. Aborted (core dumped)

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by sruthi20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1439 users visited in the last hour