File	Date	Author	Commit
GenMapWin.pl	2016-06-15	Jie Wu	[101c2b] new file: GenMapWin.pl
HMMpipe.pl	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
dnacopy.r	2016-06-07	Jie Wu	[da10ba] modified: HMMpipe.pl
findcoordinates.pl	2016-11-14	Jie Wu	[22a9f0] dnacopy findcoordinates
getGCpercent.pl	2016-06-15	Jie Wu	[101c2b] new file: GenMapWin.pl
hg19.500k.dynamic.win.bed	2016-06-15	Jie Wu	[101c2b] new file: GenMapWin.pl
hg19.500k.dynamic.win.fa.gc.txt	2016-06-15	Jie Wu	[101c2b] new file: GenMapWin.pl
hg19_gc_137k.wig	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
hg19_gc_500k.wig	2016-06-07	Jie Wu	[733a27] new file: hg19_gc_500k.wig
hg19_gc_550k.wig	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
hg19_gc_55k.wig	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
hg19_map_40mer_500k.wig	2016-06-07	Jie Wu	[200578] Initial commit
hg19_map_50mer_137k.wig	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
hg19_map_50mer_550k.wig	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
hg19_map_50mer_55k.wig	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
mm9.500k.dynamic.win.bed	2016-06-15	Jie Wu	[101c2b] new file: GenMapWin.pl
mm9.500k.dynamic.win.fa.gc.txt	2016-06-15	Jie Wu	[101c2b] new file: GenMapWin.pl
mm9_gc_137k.wig	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
mm9_gc_486k.wig	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
mm9_gc_500k.wig	2016-06-07	Jie Wu	[200578] Initial commit
mm9_gc_550k.wig	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
mm9_gc_55k.wig	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
mm9_map_40mer_500k.wig	2016-06-07	Jie Wu	[200578] Initial commit
mm9_map_50mer_486k.wig	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
normalizeGC.pl	2016-06-07	Jie Wu	[200578] Initial commit
order.txt	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
readme	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...
run_hmmcopy.hg19.r	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
run_hmmcopy.mm9.r	2021-08-20	Jie Wu	[f550a8] added new resolutions and read lengths for mm9
run_hmmcopy_new.r	2020-04-09	Jie Wu	[4671e2] updated the pipeline so that compatiable with l...

Read Me

Update Feb 2020:

Some updates for hg19:
* Newer version of HMMcopy 1.28 is now used
* 3 more resolutions added
* for older scripts, check commit in 2017

Please follow our JoVE protocol paper to run the scripts.

by kknouse at mit.edu  and jiewu at mit.edu

Prerequisites

* A unix-like environment with Perl installed.
* R with HMMcopy and DNAcopy installed.
* SAMTools 0.1.19, BWA 0.6.1, FASTX-Toolkit 0.0.13, Picard 1.94, bowtie 1.0.1 and bedtools 2.17.0.

Note: DNAcopy configuration files were generated in the following ways:

download mappablility track from ucsc goldenpath:

wget http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/wgEncodeCrgMapabilityAlign40mer.bigWig

use bigWigToWig in the kent toolkit to convert it to wiggle:

bigWigToWig wgEncodeCrgMapabilityAlign40mer.bigWig wgEncodeCrgMapabilityAlign40mer.wig

generate dynamic window:

perl GenMapWin.pl wgEncodeCrgMapabilityAlign40mer.wig >500k.dynamic.win.bed

and gc profile

bedtools getfasta -fi mm9.fa -bed 500k.dynamic.win.bed -fo 500k.dynamic.win.fa
perl getGCpercent.pl 500k.dynamic.win.fa >500k.dynamic.win.fa.gc.txt