sinto: tools for single-cell data processing
Project description
sinto
Tools for single-cell data processing
Installation
Install from PyPI:
pip install sinto
Install from source:
git clone https://github.com/timoast/sinto.git
cd sinto
python setup.py install
Features
Filter barcodes
Subsets of cells can be extracted from a BAM file 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
file
-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
Add read tags per cell
Different read tags can be added to each cell with
the sinto addtags
command.
$ sinto addtags -h
usage: sinto addtags [-h] -b BAM -f TAGFILE -o OUTPUT [-t] [-s] [-p NPROC]
[-m MODE]
Add read tags to reads from individual cells
optional arguments:
-h, --help show this help message and exit
-b BAM, --bam BAM Input bam file (must be indexed)
-f TAGFILE, --tagfile TAGFILE
Tab-delimited file containing cell barcode, tag to be
added, and tag identity. 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
file
-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
This requires a file specifying the tags to be added to each cell, for example:
TGGCAATGTTGAAGCG-1 CI A
GACCAATCACCATTCC-1 CI A
CAGGATTCAGAACTTC-1 CI B
GAACCTAAGAGAGGTA-1 CI B
ACATGGTGTAGACGCA-1 CI C
CCCTGATTCGGATAGG-1 CI C
This will add a CI
tag, with the tag set to A, B, or C depending on the cell barcode sequence.
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