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mflamand / Bullseye

Bullseye analysis pipeline for DART-seq analysis
MIT License
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How to get cell-sites matrix in scDART-seq? #15

Open MopingXu opened 3 months ago

MopingXu commented 3 months ago

Hi Mflamand, I'm running the scDART-seq data using Bullseye's pipeline, and I have some confusion: How do I get the matrix of cells and sites when there is no barcode information in the final result of single cell analysis? Or I missed some analysis? Looking forward to your reply. Best, Mope

mflamand commented 3 months ago

Hello MopingXu,

It is difficult to see what is the problem without knowing what code you are using.

The options to use will depend on the type of sequencing used and if you have individual bam files for each cell or a merged bam containing all cells.

For the latter, you would typically use use the following options "-mode SingleCell" and "-Cell_ID_pattern X" where X is "10X" (CB:Z:), "SMART" (RG:Z) or the actual string used in the BAM file for the cell ID.

If you have distinct bam files for each cell, I would invite you to look at this repo (@tegowski) for an example: https://github.com/tegowski/scDARTHEKcells

Please let me know if you have more questions.

mflamand commented 3 months ago

Hi,

The columns of the matrix file outputted by parseBAM.pl are : “chromosome, position, #A, #T, #C, #G, #N, #Total, Cell_ID”,

Best,

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Hi Mflamand,

Thank you for reply. I don't understand the result of “parseBAM.pl”, what exactly does each column mean? Best

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