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:
output.sorted.txt: information of transcripts compatible with each UMI for each cell barcode in text format
output.sorted: binary format of
matrix.ec: transcript equivalence classes in this dataset
transcripts.txt: transcripts in the transcriptome index, used in
kallistowhen generating the
These files should be sufficient to generate a sparse matrix with the package BUSpaRse. See these notebooks for how these files were generated using
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
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++.