HELP, about HPeak

[sp_wade]

Hi! I `m trying to do a peak detection using HPeak2.1.

I run the command line as following:

perl HPeak.pl -format BED -t treatment_tags.bed -c control.bed -n FoxA1

But there seems to be something wrong,the program reports a message:
"
Wed Jul 21 19:07:37 2010
##### process raw data in treated sample and get summary.
No such file or directory
Application Error: child process (summary.pl) exited abnormally.
"
However, the treatment_tags.bed and control.bed are do in the work space!
Who can tell me what `s wrong,and what should I do?
Thanks!

[sp_wade]

HI! I downloaded a 2.0 version and found a sample.
It used a media file "*.inp" to locate the treatment and control file.
So I created a media file and successfully solved the problem!
Thanks!

[Bioinfo]

Hi
I am new to ChipSeq. shall i ask you some questins regarding Hpeak? you may think is very easy however i am a newbie.
Even I have the got same error message which you had. did u tried with windows or else you tried with linux only? if so which versions of Hpeak and Illumina Pipeline. and how could we know the experiment name used (FoxA1).
thanks

[sp_wade]

HI!Bioinfo!
I tried with linux. you may try a 2.0 version first from http://www.sph.umich.edu/csg/qin/HPeak/Download.html ,and do as the manual, In the 2.0 package,there is an example folder in which includes "chip.inp" and "mock.inp". Open the .inp file ,you will find the filename of the control data or ChIP data.
you can run a command line just like this:
perl HPeak.pl -format BED -t chip.inp -c mock.inp -n sample
the format BED must be adjusted to the format of the input data, while the experiment name all depends on you!

Good luck!

Hi
I am new to ChipSeq. shall i ask you some questins regarding Hpeak? you may think is very easy however i am a newbie.
Even I have the got same error message which you had. did u tried with windows or else you tried with linux only? if so which versions of Hpeak and Illumina Pipeline. and how could we know the experiment name used (FoxA1).
thanks

[Husen]

You need to create a media/temp/text (or any file) and store path of your input data file as it's content, so content of the text file (let's name it treat.txt) may look like this:
/home/xyz/path-of-datafile/test_data.bed

to run Hpeak:
perl HPeak.pl -format BED -t treat.txt

Also consider, BED format which is required by HPeak is different from the one used by UCSC Genome browser (refer to the manual).