bam2wiggle.py - convert bam to wig/bigwig file¶
- Tags
Genomics NGS Intervals Conversion BAM WIGGLE BIGWIG BEDGRAPH
Purpose¶
convert a bam file to a bigwig or bedgraph file.
Depending on options chosen, this script either computes the densities
itself or makes use of faster solutions if possible. The script
requires the executables wigToBigWig
and bedToBigBed
to be in the user’s PATH.
If no –shift-size or –extend option are given, the coverage is computed directly on reads. Counting can be performed at a certain resolution.
The counting currently is not aware of spliced reads, i.e., an inserted intron will be included in the coverage.
If –shift-size or –extend are given, the coverage is computed by shifting read alignment positions upstream for positive strand reads or downstream for negative strand reads and extend them by a fixed amount.
For RNASEQ data it might be best to run genomeCoverageBed directly on the bam file.
Usage¶
Type:
cgat bam2wiggle --output-format=bigwig --output-filename-pattern=out.bigwig in.bam
to convert the bam file file:in.bam to bigwig format
and save the result in out.bigwig
.
Command line options¶
usage: bam2wiggle [-h] [--version] [-o {bedgraph,wiggle,bigbed,bigwig,bed}]
[-s SHIFT] [-e EXTEND] [-p SPAN] [-m]
[--scale-base SCALE_BASE] [--scale-method {none,reads}]
[--max-insert-size MAX_INSERT_SIZE]
[--min-insert-size MIN_INSERT_SIZE] [--timeit TIMEIT_FILE]
[--timeit-name TIMEIT_NAME] [--timeit-header]
[--random-seed RANDOM_SEED] [-v LOGLEVEL]
[--log-config-filename LOG_CONFIG_FILENAME]
[--tracing {function}] [-? ?] [-P OUTPUT_FILENAME_PATTERN]
[-F] [-I STDIN] [-L STDLOG] [-E STDERR] [-S STDOUT]
bam2wiggle: error: argument -?: expected one argument