Peak-finder meta server for ChIP-seq data analaysis: http://bioinf.icm.uu.se/~pfms/
developed at LCB - Uppsala University by Marcin Kruczyk and Husen M. Umer.
*************Download the distributed package (PFMS-1.3.zip)**********
--Extract
unzip -q PFMS-1.3.zip
cd PFMS-1.3/
*************Installation****************
--Section 3.2.1 in the manual (for users with root access)
sudo python setup.py install
PFMetaserver -i Input_file.bed -o test1 -bed -sissr -findpeaks -erange -max_cpu_use 2 -min_cpu 3 -quantile 80 -minFN
--Section 3.2.2 in the manual (for normal users)
python setup.py install -normal
python PFMetaserver.py -i Input_file.bed -o test1 -bed -sissr -findpeaks -erange -max_cpu_use 2 -min_cpu 3 -quantile 80 -minFN
*************Test Installation****************************
python tests.py [install-normal | install-super]
*************Test PFMS****************************
Test usage:
python tests.py input_file_path.bed output_label control_file_path.bed no-hpeak [no-macs] ... [no-hpeak] [no-findpeaks] [-super]
Or mannualy run these tests and check the output directory
--Tests:
PFMetaserver -i Input.bed -o test1-bed6 -macs -sissr -seqsite -findpeaks -cisgenome -erange
PFMetaserver -i Input.bed -control Treat.bed -o test2-bedctr6 -macs -sissr -seqsite -findpeaks -cisgenome -erange
PFMetaserver -i Input2.bed -o test3-wig4 -macs -findpeaks -cisgenome -seqsite
PFMetaserver -i Input.bed -control Treat.bed -o test4-wigctr3 -macs -findpeaks -cisgenome
*************Remove PFMS****************************
--remove the installed version: python setup.py remove