sep241mkdt#

Export deconvolution results as bigWIG files. The program produces two files: deconv_cuts-per-100bp_c1.bw and deconv_cuts-per-100bp_c2.bw for the location-marginal cut densities of channel 1 and 2, respectively.

If --unit [number] is specified, then the output file names will be deconv_cuts-per-[number]bp_c1.bw and deconv_cuts-per-[number]bp_c2.bw. The files can be used for visualization of the results using, e.g., the IGV browser or the JBrowser 2.

usage: sep241mkdt [-h] [-l LEVEL] [--logfile logfile] [-o dir] [--unit int]
                  [--region chr:start-end] [--exclude-flipped] [--span int]
                  [--no-check] [--no-progress] [--force]
                  jobdata-file chrom-sizes-file

jobdata-file#: Jobdata with cuts per interval and workchunk ids.

chrom-sizes-file#: Chromosome sizes file with the two columns: seqname and size. You can use a script like https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes to fetch the file.

-h, --help#: show this help message and exit

-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log {DEBUG,INFO,WARNING,ERROR,CRITICAL}#: Set the logging level (default=INFO).

--logfile <logfile>#: Write detailed log to this file.

-o <dir>, --out <dir>#: Output directory (default is the path of the jobdata).

--unit <int>#: Output will have the unit cuts per {unit} base pairs (default=100).

--region <chr:start-end>#: Limit output to this genomic region.

--exclude-flipped#: Exclude results from workchunks with flipped length distribution.

--span <int>#: The span of base pairs with the same value in the output bigwig (default=10).

--no-check#: Do not test for flipped length distributions.

--no-progress#: Do not show progress.

--force#: Make bigwigs even if some results are missing.