scExportSignal#
scExportSignal exports sincei-supported .h5ad (anndata) file to other formats.
usage:
scExportSignal -i INPUT.h5ad --outFileFormat FORMAT -o OUTPUT
Input/Output options#
- --input, -i
sincei-generated input file in .h5ad format.
- --outFilePrefix, -o
Prefix for output file names.
Common Options#
- --outFileFormat
Possible choices: bm, mtx, loom
Output file format for scExportSignal. "bm" refers to the BedGraphMatrix format, useful for single-cell data visualization with pyGenomeTracks. It stores data in dense format, so we recommend choosing a region to export instead of the whole dataset. "mtx" refers to the MatrixMarket sparse-matrix format. The output in this case would be <prefix>.counts.mtx, along with <prefix>.rownames.txt and <prefix>.colnames.txt . "loom" refers to the Loom file format, which is a legacy single-cell sparse-matrix format. Note: conversion to loom requires loompy, which is not installed by default. You may install it by running
pip install loompy.- --region, -r
Region of the genome to export. The format is chr:start:end, for example
--region chr10or--region chr10:456700:891000.
Other options#
- --verbose, -v
Set to see processing messages.
- -V, --version
Print the program version and exit.