(a) is the default in the current release of ERANGE.
Simply proceed to RUNNING THE PEAK FINDER for (a) and
(a) is the default in the current release of ERANGE.
Simply proceed to RUNNING THE PEAK FINDER for (a) and
flag with findall.py. For (c), use weighMultireads.py
to weigh multireads based on a unique reads in the
respective radius of each potential location. Once run,
flag with findall.py. For (c), use weighMultireads.py
to weigh multireads based on a unique reads in the
respective radius of each potential location. Once run,
which will run the peak finder on chip.rds / control.rds ,
store the enriched region coordinates in chip.regions.txt,
which will run the peak finder on chip.rds / control.rds ,
store the enriched region coordinates in chip.regions.txt,
You will *NEED* to change some of the default parameters
if working in smaller genomes (e.g. use smaller -spacing),
if working with certain types of IPs such as histones and
You will *NEED* to change some of the default parameters
if working in smaller genomes (e.g. use smaller -spacing),
if working with certain types of IPs such as histones and
-polymerases (test with and without -notrim and
--nodirectionality), if working with rather weak IPs
-(e.g. -minimum and -ratio), or if working with larger
+polymerases (test with and without --notrim and
+--nodirectionality), if working with rather weak IPs
+(e.g. --minimum and --ratio), or if working with larger
fragment sizes (see the paragraph below discussing read
shifting).
findall.py returns a per-peak p-value. By default, this
is calculated using a Poisson distribution of peak RPMs
fragment sizes (see the paragraph below discussing read
shifting).
findall.py returns a per-peak p-value. By default, this
is calculated using a Poisson distribution of peak RPMs
By default, findall.py does not try to adjust the location
of the reads based on half the size of the expected fragment
length (the "shift"). If you believe that you need to shift
your peaks, findall.py can try to pick the best shift based
on the best shift for strong sites using the parameter
By default, findall.py does not try to adjust the location
of the reads based on half the size of the expected fragment
length (the "shift"). If you believe that you need to shift
your peaks, findall.py can try to pick the best shift based
on the best shift for strong sites using the parameter
-'-shift learn '. You can also either manually specify a
-shift value using '-shift #bp ' or ou can calculate a
-"best shift" for each region using '-autoshift'. If you
+'--shift learn '. You can also either manually specify a
+shift value using '--shift #bp ' or ou can calculate a
+"best shift" for each region using '--autoshift'. If you
peak a shift if there are at least 30 regions that meet
its training criteria.
(ii) if (i) couldn't pick a shift, run findall.py with
peak a shift if there are at least 30 regions that meet
its training criteria.
(ii) if (i) couldn't pick a shift, run findall.py with
local caching, where is as large as appropriate as
described in section 9 of README.build-rds .
local caching, where is as large as appropriate as
described in section 9 of README.build-rds .
version 3.1 February 2009 - support for read shifting
version 3.0 February 2009 - support for UCSC narrowPeak format in regiontobed.py
version 3.0rc1 December 2008 - added parameter to control peak-trimming
version 3.1 February 2009 - support for read shifting
version 3.0 February 2009 - support for UCSC narrowPeak format in regiontobed.py
version 3.0rc1 December 2008 - added parameter to control peak-trimming