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amcpherson committed Jul 18, 2017
1 parent 5ff06a3 commit 5911bf69f11d8d185f7054098d39799d2c6894cc
Showing with 12 additions and 12 deletions.
  1. +12 −12 README.md
@@ -27,16 +27,16 @@ Should result in main binaries in /bin and useful binaries in /util
Overview:
mapCounter is a small program for calculating average mappability[1][1] for non-overlapping
windows of fixed width across all sequences (i.e. chromosomes) present in a BigWig file[2].
It is built mainly on top of an independent subset of files obtained from the UCSC Genome
Browser source code (i.e. kent library)[3] made available by Jim Kent. Generating average
mappability files in 1000 base windows (default) on hg18 took 160 seconds on a 3.06 GHz Intel
Core 2 Duo with 8GB RAM.
mapCounter is a small program for calculating average [mappability] for non-overlapping
windows of fixed width across all sequences (i.e. chromosomes) present in a [BigWig file].
It is built mainly on top of an independent subset of files obtained from the
[UCSC Genome Browser source code] (i.e. kent library) made available by Jim Kent.
Generating average mappability files in 1000 base windows (default) on hg18 took 160
seconds on a 3.06 GHz Intel Core 2 Duo with 8GB RAM.
[1]: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeMapability
[2]: http://genome.ucsc.edu/goldenPath/help/bigWig.html
[3]: http://genome.ucsc.edu/admin/git.html
[mappability]: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeMapability
[BigWig file]: http://genome.ucsc.edu/goldenPath/help/bigWig.html
[UCSC Genome Browser source code]: http://genome.ucsc.edu/admin/git.html
Features:
@@ -90,10 +90,10 @@ Fast and memory efficient counting of reads in BAM files
Overview:
mapCounter is a small program for counting the number of reads in non-overlapping
windows of fixed width directly from BAM files. It is build on top of the BamTools
API[1] made available by Derek Barnett on GitHub (https://github.com/pezmaster31/bamtools).
windows of fixed width directly from BAM files. It is build on top of the [BamTools API]
made available by Derek Barnett on GitHub (https://github.com/pezmaster31/bamtools).
[1] http://bioinformatics.oxfordjournals.org/content/27/12/1691
[BamTools API]: http://bioinformatics.oxfordjournals.org/content/27/12/1691
Features:

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