The input is missing. I just checked the test command, its

java -jar FindPeaks.jar -input 22.test.eland -output /output/directory/ -eff_frac 1.0 -dist_type 1 200 -directional -filter -hist_size 200

It will be fine for mm9, just change the format for file that you are inputting in the aligner parameter. Read Wiki for more examples.

the above reply from sukhdeep gave me the error :aligner type must be provided with the -aligner flag also directional and filter flags could not be processed.; since it is not taking eland as default.So,i had to add also -aligner eland and remove directional filter from the cmd Maybe earlier versions reqd these flags.

changing these gave two regions as peaks and a wig.gz file to my output directory.

The peaks file have the format : idchromstartendmax_coord;

so i guess now its ok. will try the sam files to check it out and post any problems which arise.

thanks for the info. sumon.

Hi,

I had two bam files oct4 and gfp (mapping to only chr1 of mm9 genome) which I wanted to analyze with FindPeaks 4.0.Setting -Xmx2G always java VM failed but i have 4gb ram windowsxp(32bit), maybe it cant allocate even half. so I used the cmd:

java-Xmx 1500m -jar FindPeaks.jar -name xyz -disttype 1 200 -subpeaks 0.2 -bedgraph -efffrac 0.7 -output C:/ -input chip.bam -compare control.bam -aligner sam

I got some png files regions graph as output viz: pregraph,first graph,second graph with lines drawn are they regression lines with equations how do interpret them? plus wig files (wig files one for ctrl and one for sample) , but only one bedgraph file?

Which file in the following should I use as the peak file among the following:

a) xyz triangle subpeaks with id,chrom,start,end and max coord or b) xyz traingle subpeaks filtered sample peaks file with id,chrom,start,end,max cord, height,prob sequence

Could anybody elucidate slightly or suggest further tuning parameters to improve the output

sumon

Hi, I have a question regarding the -iterations and -landerwaterman options. I read that the landerwaterman options best with disttype 0 as it performs poorly with weighted (-disttype 1) distributions and the native/PET (-dist_type 3) distributions.

a)Is the value of integer following dist_type 0 the tag length like 26 reads or 36 reads that we provide in MACS ? b)Can i use both options together in a command ?

suman