From: Tim Reddy Tim <treddy@hudsonalpha.org>
Date: Mon, 5 Jan 2009 17:20:11 +0000 (+0000)
Subject: Change over from wiggle files to bedgraph files to profile reads. Reasons are
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=5b17a2fe51efbed60f43e65485cf34ff8f3a6d69

Change over from wiggle files to bedgraph files to profile reads. Reasons are
1) Wiggle files at some point exceed the amount of data that ucsc will accept
2) Bedgraph is more accurate, I think
3) Also, used this as an opportunity to put strand direction on profiles, so now two tracks
   are made, one for forward strand reads, one for reverse strand reads.
---

diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm
index d4348c8..183d060 100755
--- a/htswanalysis/scripts/ConfigureTasks.pm
+++ b/htswanalysis/scripts/ConfigureTasks.pm
@@ -235,7 +235,7 @@ sub WriteProfileTasks {
 
       my $seqcheck = "if [ ! -e $data_dir/Libraries/$lib.txt ]; then $root_dir/scripts/analys_track_main.py updsts $task \"Waiting for sequencing.\"; fi;"; 
       my $cmds .= "$lib.wig.gz: $data_dir/Libraries/$lib.txt\n";
-      $cmds .= "\t".$PROFILEDIR.'/profile_reads_wig '.$data_dir.'/Libraries/'.$lib.'.txt "'.$name.'" "'.$name.'" | gzip > '.$lib.'.wig.gz';
+      $cmds .= "\t".$PROFILEDIR.'/profile_reads_bedgraph '.$data_dir.'/Libraries/'.$lib.'.txt "'.$name.'" "'.$name.'" | grep -v contam | grep -v Ribo | grep -v splice | gzip > '.$lib.'.wig.gz';
       $cmds .= "\n\n";
       $cmds .= $lib.'.profile.gif: '.$data_dir.'/Libraries/'.$lib.'.txt '.$root_dir.'/reference_data/'.$genome.'_tx_start_sites'."\n";
       $cmds .= "\t".$PROFILEDIR.'/profile_reads_against_features $^ | '.$root_dir.'/scripts/profile_to_svg.pm | /opt/local/bin/convert - $@'."\n";