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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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Program aborted #5

Open dauss75 opened 4 years ago

dauss75 commented 4 years ago

Hello,

I've got the following problems. Could you comment on that?

Thanks, Segun

cmd: msisensor2 msi -M models_hg19 -t our_tumor.bam -o test

loading homopolymer and microsatellite sites ...

Total loading windows: 1435

Total loading homopolymer and microsatellites: 2797

Program aborted: Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!

Beifang commented 4 years ago

It probably was caused by the chromosomes format in the input hg19 bam file. Please make sure the chromosomes in the input bam like: chr1, chr2 ... instead of 1,2...

dauss75 commented 4 years ago

Thanks. Could I build the model myself for hg19?

Beifang commented 4 years ago

The training process using total ~2 million sites is relatively complex and time consuming. We can train the a panel-specific model for you if you provide us a bed file with regions of interest, any particular microsatellites or sequencing data.

Young-Matthew commented 4 years ago

The training process using total ~2 million sites is relatively complex and time consuming. We can train the a panel-specific model for you if you provide us a bed file with regions of interest, any particular microsatellites or sequencing data.

Hi, I do need to customize panel model. How can I contact you to send the materials for training process ?

Beifang commented 4 years ago

please reach Xinyin Han by : hanxinyin@cnic.cn