Etchevers:Notebook/STRA6 in eye development/2009/09/02

{| width="800"
 * style="background-color: #EEE"|[[Image:C14.jpg|128px]] Genetics of human eye development
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


 * colspan="2"|
 * colspan="2"|

New release Sept 1st of FP 4.0.5
Yesterday's installation attempt was from "Révision 1496 extraite".

Today's yields "Révision 1516" instead - so let's see how progress is. First difference - "Compiling 157 source files to /home/heather/trunk/classes"

then

buildall:

BUILD SUCCESSFUL

Total time: 6 seconds

Yay!

Now load up the Fasteris data and try something out.

Example updated by Andrew on his workflows page:

''time java -Xmx2G -jar FindPeaks.jar -name test -input /path/to/*.part.eland.gz -output /output_path/ \ -aligner eland -one_per -dist_type 1 200''

' You may need to add the optional "-prepend chr" tag, if your chromosome names/numbers do not contain this prefix.'

Some simple parameter changes of interest:

* to prevent singleton mapping reads from appearing, you can use a minimum height cutoff (-minimum 2) * '''if histograms are not required, they can be turned off by setting histogram size to 1. (-hist_size 1)''' * if you know the exact size of each read, you can use a fixed length extension (-dist_type 0 ) \ or use the size of the sequence itself (-dist_type 3) * multiple peaks can be identified in complex regions for peaks files (-subpeaks ) [not for me]

The BED example he gave was:

you@machine:/path$ java -Xmx2G -jar /home/fejes/workspace/Vancouver_Package/jars/fp4/FindPeaks.jar \ -input out/*.part.bed.gz -aligner bed -output wig/ -dist_type 1 -name example -one_per


 * Heather 04:14, 2 September 2009 (EDT):

I might need to make sure all the files and pathnames are actually installed ON the lab computer rather than reading them off the DVD. Yes, the files are the original downloads. I hope they are all okay, as if I remember right some of the downloads were incomplete.

Here was one of the last example entries, to modify and try again:

time java -Xms2G -Xmx11G -jar ~/trunk/jars/fp4/FindPeaks.jar -name PAX6-RAX-FP-Chr17 -input /home/oeil/Documents/Fasteris_7_2009/GDZ5_PAX6_bed/PAX6_Chr17.bed -compare /home/oeil/Documents/Fasteris_7_2009/GDZ4_RAX_bed/RAX_Chr17.bed -aligner bed -dist_type 3 -minimum 20 -min_ht_process 3 -compare /home/oeil/Documents/Fasteris_7_2009/GDZ4_RAX_bed/RAX_Chr17.bed -alpha 0.05 -max_pet_size 1000 -output /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17

First, how much swap memory did I specify? 8 Go. (Whew).

Unpack and organize files then can resume this.


 * }