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robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool
qb.cshl.edu/ginkgo
BSD 2-Clause "Simplified" License
47 stars 28 forks source link

How to define the reference sample? #8

Closed anyone1985 closed 6 years ago

anyone1985 commented 6 years ago

I have some MALBAC single cell data. I'd like to analyze the CNV with ginkgo. I do not know how to define the normal sample in the config file. Please give me some example to follow.

tgarvin commented 6 years ago

Hi. You need to also provide Malbac single cell read data in bed format for a cell that you know is from normal diploid tissue (I.e. from a tissue that has no major copy number variations).

If you didn't sequence any cells from a known normal diploid cell line you can download sequencing data from any previously generated dataset in the same organism/cell line. However, it's always better to have data from the same sequencing runs to control for any other errors introduced in the process.

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I have some MALBAC single cell data. I'd like to analyze the CNV with ginkgo. I do not know how to define the normal sample in the config file. Please give me some example to follow.

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anyone1985 commented 6 years ago

Yeah. I have malbac single cell data from blood and adjacent. How do I define this data in the config file? Another question is if ginkgo could output the range of LOH. Because I need this data for SciClone analysis ? Thank you for your quick reply.

robertaboukhalil commented 6 years ago

In the GUI, under Segmentation, select Custom and upload the reference .bed file.

If you're using the CLI, you can define segMeth=2 and ref=yourRefFile.bed in the config.

Let us know if that fixes your issue.

anyone1985 commented 6 years ago

Thank you for your answer.