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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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Run monopogen for more than 1 sample? #43

Closed ZhengJIN94 closed 2 months ago

ZhengJIN94 commented 4 months ago

Hi,

I have run preprocess and germline calling steps for 9 scRNA-seq samples (10x genomics data).

Now, I hope to call somatic mutation, and I have a question about the cell barcode files.

How should I prepare the cell barcode file? Put all cells of 9 samples in one file?

However, in 10x genomics data, if we do not add index to cell barcode, there will be several duplication barcodes, can monopogen recognize the index part (such as AAACCCAAGCATTTGC-1_1_1_1_1_1 or sample1_AAACCCAAGCATTTGC-1) ?

Or, I should run it one by one from the initial (preprocess) step?

Thank you, so much!

jinzhuangdou commented 4 months ago

You use joint-calling mode for germline calling or run germline calling one by one?

If you want to call somatic SNVs, you need to run germline module for each sample (i.e, only set one sample in bam.lst).

jinzhuangdou commented 4 months ago

In such case, you need to prepare bam.S1.lst, bam.S2.lst, ..., bam.S9.lst.