sinto：单单元数据处理工具
sinto的Python项目详细描述
辛托
单细胞数据处理工具
安装
从pypi安装：
pip install sinto
从源安装：
git clone https://github.com/timoast/sinto.git
cd sinto
python setup.py install
功能
过滤条形码
可以使用
sinto filterbarcodes命令：
$ 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
为每个单元格添加读取标记
可以将不同的读取标记添加到每个单元格
sinto addtags命令。
$ 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
这需要一个指定要添加到每个单元格的标记的文件，例如：
TGGCAATGTTGAAGCG-1 CI A
GACCAATCACCATTCC-1 CI A
CAGGATTCAGAACTTC-1 CI B
GAACCTAAGAGAGGTA-1 CI B
ACATGGTGTAGACGCA-1 CI C
CCCTGATTCGGATAGG-1 CI C
这将添加一个CI标记，根据单元格条形码序列，标记设置为a、b或c。
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