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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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MSISensor distribution file only has 10+ base repeats. Where are datapoints for di-tri-quad-penta, etc repeats? #21

Closed ranasats closed 1 week ago

ranasats commented 3 years ago

I'm looking at MSI Sensor output distribution file.

All of the lines in my output are at minimum 10 base repeats, but nothing that are 2 to 9 base repeats.

For example:

1 993467 GTTTC 10[A] TGAAA

is the smallest base pair repeat that is in the distribution file. There are none that are 9bp and below

Is there anyway to get this data?

PengJia6 commented 3 years ago

@ranasats please set -l option when you use scan and msi module!

ruolin commented 3 years ago

I have the same problem. The -l option is disabled in msisensor pro, line 480 here https://github.com/xjtu-omics/msisensor-pro/blob/master/cpp/distribution.cpp#L480. The -p does not change the lower bound. Also, it is not clear to me what is the difference between MininalHomoForDis and MininalHomoSize.

PengJia6 commented 1 week ago

I apologize for the delayed response. If you are still using it, please check version 1.3.0; this issue should have been resolved.