README.md

In BUStools/TENxBUSData: Single cell dataset from 10x in BUS format

TENxBUSData

This package is a thin wrapper to download 5 differrent 10x datasets in the BUS format, from within R. For each dataset, the following files will be downloaded:

1. output.sorted.txt: information of transcripts compatible with each UMI for each cell barcode in text format
2. output.sorted: binary format of output.sortedd.txt
3. matrix.ec: transcript equivalence classes in this dataset
4. transcripts.txt: transcripts in the transcriptome index, used in kallisto when generating the bus format

These files should be sufficient to generate a sparse matrix with the package BUSpaRse. See these notebooks for how these files were generated using kallisto and bustools and how we can generate a sparse matrix from these files.

The main purpose of this package, and the package BUSpaRse, is for advanced users to experiment with different ways to collapse UMIs mapped to multiple genes, to error correct barcode, or to adapt the BUS format for other purposes. The most recent version of kallisto and bustools should suffice to generate the gene count matrix from FASTQ files. You may also do so with BUSpaRse, but it's less efficient than using bustools. However, it's easier to tweak code from BUSpaRse than that from bustools for experimentation because R and Rcpp are easier to work with than pure C++.

BUStools/TENxBUSData documentation built on May 8, 2020, 4:20 a.m.