- Counts at each position for the plus/forward strand of each chromosome
- Counts at each position for the minus/reverse strand of each chromosome
where OUTBASE is given by the user.
show this help message and exit
Base name for output files
Size of nucleotides to fetch at once for export. Large values are faster but require more memory (Default: 100000)
Suppress all warning messages. Cannot use with ‘-v’.
Increase verbosity. With ‘-v’, show every warning. With ‘-vv’, turn warnings into exceptions. Cannot use with ‘-q’. (Default: show each type of warning once)
Count & alignment file options¶
Open alignment or count files and optionally set mapping rules
--count_files COUNT_FILES [COUNT_FILES ...]
One or more count or alignment file(s) from a single sample or set of samples to be pooled.
Format of file containing alignments or counts (Default: BAM)
Whether counts should be normalized to counts per million (usually not. default: False)
Sum used in normalization of counts and RPKM/RPNT calculations (Default: total mapped reads/counts in dataset)
Minimum read length required to be included (BAM & bowtie files only. Default: 25)
Maximum read length permitted to be included (BAM & bowtie files only. Default: 100)
Maximum desired memory footprint in MB to devote to BigBed/BigWig files. May be exceeded by large queries. (Default: 0, No maximum)
Use slower but memory-efficient implementation for big genomes or for memory-limited computers. For wiggle & bowtie files only.
Alignment mapping functions (bam & bowtie files only)¶
For BAM or bowtie files, one of the mutually exclusive read mapping functions is required:
Map read alignment to a variable offset from 5’ position of read, with offset determined by read length. Requires –offset below
Map read alignment to 5’ position.
Map read alignment to 3’ position
Subtract N positions from each end of read, and add 1/(length-N), to each remaining position, where N is specified by –nibble
Filtering and alignment mapping options¶
The remaining arguments are optional and affect the behavior of specific mapping functions:
For –fiveprime or –threeprime, provide an integer representing the offset into the read, starting from either the 5’ or 3’ end, at which data should be plotted. For –fiveprime_variable, provide the filename of a two-column tab-delimited text file, in which first column represents read length or the special keyword ‘default’, and the second column represents the offset from the five prime end of that read length at which the read should be mapped. (Default: 0)
For use with –center only. nt to remove from each end of read before mapping (Default: 0)
Browser track options¶
An RGB hex string (‘#NNNNNN’, N in [0-9,A-F]) specifying the track color.
Name to give browser track
Format of output file (Default: bedgraph)
main(argv=['-T', '-E', '-b', 'readthedocs', '-d', '_build/doctrees-readthedocs', '-D', 'language=en', '.', '_build/html'])¶
- argv : list, optional
A list of command-line arguments, which will be processed as if the script were called from the command line if
main()is called directly.
Default: sys.argv[1:] (actually command-line arguments)