Unable to establish baseline

[zsy3]

Hi,

I used your test case, the program reported the following error "unsufficient number of samples in model:MSINR21_MSS: 1 samples, MSINR21_MSI: 0 samples"

I am wondering how to establish a baseline? How many samples are needed to establish a baseline? Or can you provide an established baseline for us to use?

Thanks

[fescudie]

Hi,

The minimum number of MSI and MSS samples required for model creation is 10: 10 MSI and 10 MSS. You can change this minimum value with the argument ---min-support-samples.

For a real dataset, you are encouraged to have more samples to train your model. For the test dataset it is necessary to set this value to 1 because it contains only 2 samples (you can see an example of command line for this dataset on line 41 in miams/test/check_model_creation.sh).

This value can also be reduced when you try you first models for your panel.

Kind regards

[zsy3]

Hi,
thank you for your reply. I tried to establish a baseline with the following content, but the program reported an error. So I wonder if you can provide an established baseline for us to use?

Thanks

sample chr2_61187478 chr4_79781169 chr15_73567137 chr2_197654578 chr8_141293914 chr14_96800846
ILMN09_MSI MSI MSI MSI MSI MSI MSI
ILMN01_MSS MSS MSS MSS MSS MSS MSS

[fescudie]

Hi,

The link between your samples names in the BED file and the fastq is retrieved by searching the name from the BED in the fastq basename. In your case, "ILMN01_MSS" does not match with the file "ILMN01.end1.fq.gz". It is necessary to remove "_MSS" from your sample name in the BED file.

I cannot provide you a baseline and model file because they depend on your amplicons design. The learning step records amplicons coordinates (from BED) and size distribution (from your reads) for each status.

Kind regards

[zsy3]

Hi,
Thank you very much for your reply. This time I removed the "_MSS", but the following error occurred in the program.

I really don't know how to solve it, can you provide some ideas?

Thanks

[fescudie]

Hi,

Could you provide me the result of the following command: ${APP_DIR}/jflow/bin/jflow_admin.py status --workflow-id 12 ? The result should identify the failed step.

Have a nice day.