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mcvickerlab / WASP2

Allele-specific pipeline for unbiased read mapping(WIP), QTL discovery(WIP), and allelic-imbalance analysis
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Example for barcodes files. #1

Open fanyue322 opened 2 years ago

fanyue322 commented 2 years ago

Hi

Thanks for your great tool.

I want to perform ASE calling from 10X scRNA-seq data. Is there an example file for barcodes file(barcodes and their group/cell mapping) so that I can follow the tutorial? Many thanks.

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AaronJeeHo commented 2 years ago

Hello,

Thank you the interest in the software!

The barcode file is a two column tsv with the first column denoting barcode, and the second barcode denoting some form of grouping (ie. Cell-Type / Clusters). This file should not include a header.

Format...

CACCCAAGTGAGTTGG-1  Oligodendrocytes
GCTTAAGCCGCGGCAT-1  Oligodendrocytes
GTCACGGGTGGCCTAG-1  Endothelial
GCGATCGAGGCTTAAA-1  Oligodendrocytes
TACTCGCGTACGGTTG-1  OPC

Since the software is still very much in pre-development, the single cell pipeline in particular will go through a lot of changes. In the future it hopefully should be easier to work with 10x data, and the required inputs may change.

A formal tutorial with examples, seem like a useful thing to have. I'll look to include these in the future as I continue to improve the documentation.

Thanks!