Hi all,
I just posted Version 2.9.0. The details of the release are below. Highlights include a new unionBedGraphs tool, a "per-base" coverage option for coverageBed, a "distance" option for closestBed, and multi-column operations for groupBy.
Best,
Aaron
=== New tools ===
1. unionBedGraphs. This is a powerful new tool contributed by Assaf Gordon from CSHL. It will combine/merge multiple BEDGRAPH files into a single file, thus allowing comparisons of coverage (or any text-value) across multiple samples. The example below illustrates how to compare coverage across three different BEDGRAPH files.
=== New features ===
1. The "groupBy" tool now allows one to operate on multiple columns for each group. For example:
2. New "distance feature" (-d) added to closestBed by Erik Arner. In addition to finding the closest feature to each feature in A, the -d option will report the distance to the closest feature in B. Overlapping features have a distance of 0.
3. New "per base depth feature" (-d) added to coverageBed. This reports the per base coverage (1-based) of each feature in file B based on the coverage of features found in file A. For example, this could report the per-base depth of sequencing reads (-a) across each capture target (-b).
Best,
Aaron
I just posted Version 2.9.0. The details of the release are below. Highlights include a new unionBedGraphs tool, a "per-base" coverage option for coverageBed, a "distance" option for closestBed, and multi-column operations for groupBy.
Best,
Aaron
=== New tools ===
1. unionBedGraphs. This is a powerful new tool contributed by Assaf Gordon from CSHL. It will combine/merge multiple BEDGRAPH files into a single file, thus allowing comparisons of coverage (or any text-value) across multiple samples. The example below illustrates how to compare coverage across three different BEDGRAPH files.
Code:
$ cat 1.bg chr1 1000 1500 10 chr1 2000 2100 20 $ cat 2.bg chr1 900 1600 60 chr1 1700 2050 50 $ cat 3.bg chr1 1980 2070 80 chr1 2090 2100 20 $ unionBedGraphs -header -i 1.bg 2.bg 3.bg -names WT-1 WT-2 KO-1 chrom start end WT-1 WT-2 KO-1 chr1 900 1000 0 60 0 chr1 1000 1500 10 60 0 chr1 1500 1600 0 60 0 chr1 1700 1980 0 50 0 chr1 1980 2000 0 50 80 chr1 2000 2050 20 50 80 chr1 2050 2070 20 0 80 chr1 2070 2090 20 0 0 chr1 2090 2100 20 0 20
=== New features ===
1. The "groupBy" tool now allows one to operate on multiple columns for each group. For example:
Code:
$ cat ex1.out chr1 10 20 A chr1 15 25 B.1 1000 chr1 10 20 A chr1 25 35 B.2 10000 $ groupBy -i ex1.out -grp 1,2,3,4 -opCols 8,9 -ops collapse,mean chr1 10 20 A B.1,B.2, 550
3. New "per base depth feature" (-d) added to coverageBed. This reports the per base coverage (1-based) of each feature in file B based on the coverage of features found in file A. For example, this could report the per-base depth of sequencing reads (-a) across each capture target (-b).
Best,
Aaron
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