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sinto: tools for single-cell data processing

Project description


Tools for single-cell data processing


git clone
cd sinto
python install


Filter barcodes

If you want to extract reads from a subset of cell barcodes, you can do so using the sinto filterbarcodes command.

$ sinto filterbarcodes -h
usage: sinto filterbarcodes [-h] -b BAM -c CELLS -o OUTPUT [-t] [-s]
                            [-p NPROC] [-m MODE]

Filter reads based on input list of cell barcodes

optional arguments:
  -h, --help            show this help message and exit
  -b BAM, --bam BAM     Input bam file (must be indexed)
  -c CELLS, --cells CELLS
                        File or comma-separated list of cell barcodes. Can be
                        gzip compressed
  -o OUTPUT, --output OUTPUT
                        Name for output text file
  -t, --trim_suffix     Remove trail 2 characters from cell barcode in BAM
  -s, --sam             Output sam format (default bam output)
  -p NPROC, --nproc NPROC
                        Number of processors (default = 1)
  -m MODE, --mode MODE  Either tag (default) or readname. Some BAM file store
                        the cell barcode in the readname rather than under a
                        read tag

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