https://sourceforge.net/p/hpeak/wiki/Home/Recent changes to HomeenFri, 25 Jan 2013 20:34:24 -0000https://sourceforge.net/p/hpeak/wiki/Home/<div class="markdown_content"><p>HPeak usage:<br /> Command (single-end):<br /> perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles<br /> Command (pair-end):<br /> perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles<br /> note:<br /> 1. Default species is HUMAN. Also supports MOUSE. Can add any other genome if in need. <br /> 2. Default format is BED. Also support ELAND. Will add SAM and BAM. <br /> 3. –r specifies read length (this is import through my experience). <br /> 4. –pe indicates pair-ended data. <br /> 5. If data is pair-ended, -isize refers to insert size (total length of a pair).<br /> 6. By default, control data is pair-ended if treatment data is pair-ended. Use “-sec” <br /> if the control data is single-ended for pair-end ChIP data. </p></div>peterbengkuiFri, 25 Jan 2013 20:34:24 -0000https://sourceforge.nete1d5735e78c4bdf5e2ab223fccf83989cc0ad48ahttps://sourceforge.net/p/hpeak/wiki/Home/Welcome to your wiki! This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/hpeak/wiki/markdown_syntax/) syntax. [[project_admins]] [[download_button]] peterbengkuiWed, 30 May 2012 19:51:41 -0000https://sourceforge.net173f0e07fc54853215e2720e89819c2ddf800e1b