steinmann / peakzilla Goto Github PK

I would like to put a wrapper into the galaxy tool shed, but this is only possible with a correct license

Dear Jonas ,

Greetings for the day !!!

I have chip-exo data. To call peak, I am planning to used peakzilla.
Before trying out on our lab data, my boss wants me to replicate the result published in peakzilla paper.

I have three bam file for three replicates of CTCF data from Rhee and Pugh,2011. I run Peakzilla with default parameter,

Below are the results I got

But in publication, you have mentioned 36 bp peak and 60 smallest peak to peak distance.

I think it may be the peakzilla version which I am using is different than used during publication.

Can you please explain to me why I am getting such results.

Command used:

python ~/Tools/peakzilla-master/peakzilla.py input.bed >$out"s1_peaks.tsv"

Best Regards,
Sudhir

It would be nice if peakzilla could directly load bam files

I'm happy to provide data files separately.

$ python peakzilla/peakzilla.py ip.bed bg.bed
Traceback (most recent call last):
  File "peakzilla/peakzilla.py", line 817, in <module>
main()
  File "peakzilla/peakzilla.py", line 89, in main
peak_model = PeakShiftModel(ip_tags, options)
  File "peakzilla/peakzilla.py", line 368, in __init__
self.build()
  File "peakzilla/peakzilla.py", line 381, in build
top_shifts.append(self.peak_shifts[i][1])
IndexError: list index out of range
$ uname -a
Darwin  12.4.0 Darwin Kernel Version 12.4.0: Wed May  1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 i386 MacBookPro9,2 Darwin
$ python --version
Python 2.7.5
$ 

Dear Jonas,

Thank you for coding such a great tool for peak calling. It will greatly
contribute to my graduate project.

I would like to ask couple questions. I would like to process a public GEO
dataset that contains chip-exo data. Each sample contains two bed files (
for paired ends reads). therefore can I use peakzilla to call peaks as it
was advertised in the abstract of peakzilla paper ? If so could you
describe me how ? because in github tutorial there is only single end read
run is shown.

Best regards,

Tunc.