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calc_fixedstep
calc_fixedstep uses BED, PSL, or other entries in the data stream containing chromosome coordinates to create fixedstep entries from the SCORE field. The entries can be output with write_fixedstep or used for the creation of Wiggle tracks in the UCSC genome browser with upload_to_ucsc.
The fixedstep scores are calculated as the sum of the SCOREs of overlapping entries:
========== BED entry1 Q_ID 1
========== BED entry2 Q_ID 2
========== BED entry3 Q_ID 3
136666666653 fixedstep scores
If there is no SCORE field, 1 is used:
========== BED entry1
========== BED entry2
========== BED entry3
123333333321 fixedstep scores
See the Examples section for more details.
For more about fixedstep and Wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
... | calc_fixexstep [options]
[-? | --help] # Print full usage description.
[-C | --check] # Check the integrity of the records.
[-l | --log10] # Use log10 fixedstep scores.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following BED entries in the file test.bed:
chr1 10 20
chr1 11 21
chr1 12 22
To calculate fixedstep entries first read them in with read_bed:
read_bed -i test.bed | calc_fixedstep
STEP: 1
CHR_BEG: 10
VALS: 1;2;3;3;3;3;3;3;3;3;2;1
CHR: chr1
REC_TYPE: fixed_step
---
If the BED entries contain a SCORE field it is used for calculating the fixedStep values. Consider the following BED entries in test.bed:
chr1 10 20 idA 1
chr1 11 21 idB 2
chr1 12 22 idC 3
read_bed -i test.bed | calc_fixedstep
STEP: 1
CHR_BEG: 10
VALS: 1;3;6;6;6;6;6;6;6;6;5;3
CHR: chr1
REC_TYPE: fixed_step
---
To output the fixedstep entries use write_fixedstep.
To create a Wiggle track in the UCSC genome browser use upload_to_ucsc.
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2008
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
calc_fixedstep is part of the Biopieces framework.