cont 11b analysis

dge_workflow/bowtie2_qc.R

@@ -39,7 +39,7 @@ parseAlgnSummary <- function(alignSummary){
     algnData <- readLines(alignSummary)
 
     data.frame(
-        condition=trimEnd(basename(alignSummary), logSuffix),
+        sample=trimEnd(basename(alignSummary), logSuffix),
         num_reads=as.numeric(str_split_fixed(algnData[1], " ", 2)[1]),
         mapping_efficiency=as.numeric(str_replace(str_split_fixed(algnData[6], " ", 2)[1], "%", "")),
 
@@ -58,23 +58,23 @@ scale_fill_discrete <- function (...){ scale_color_brewer(..., type = "seq", pal
 
 
 #+ fig.height=nrow(algnSummary)/3
-ggplot(algnSummary, aes(condition, mapping_efficiency)) +
+ggplot(algnSummary, aes(sample, mapping_efficiency)) +
     geom_bar(stat="identity") +
     coord_flip() +
     ylim(0,100) +
     ggtitle("mapping efficiency")
 
-ggplot(algnSummary, aes(condition, num_reads)) +
+ggplot(algnSummary, aes(sample, num_reads)) +
     geom_bar(stat="identity") +
     coord_flip() +
     ggtitle("read counts") +scale_y_continuous(labels=comma)
 
-ggplot(algnSummary, aes(condition, unique_mapper_prop)) +
+ggplot(algnSummary, aes(sample, unique_mapper_prop)) +
     geom_bar(stat="identity") + coord_flip() +
     ggtitle("unique-mapper proportions") +
     scale_y_continuous(labels=comma)
 
-ggplot(algnSummary, aes(condition, multi_mappers_prop)) +
+ggplot(algnSummary, aes(sample, multi_mappers_prop)) +
     geom_bar(stat="identity") + coord_flip() +
     ggtitle("multi-mapper proportions") +
     scale_y_continuous(labels=comma)

dge_workflow/dge_master_template.sh

@@ -3,7 +3,11 @@ export project=<<PROJECTNAME>>
 # screen -R $project
 
 
-export DGE_HOME=/sw/users/brandl/projects/<<PROJECTNAME>>
+## intially
+DGE_HOME=/projects/bioinfo/holger/bioinfo_templates/dge_workflow
+## when customization is needed
+#export DGE_HOME=/sw/users/brandl/projects/<<PROJECTNAME>>
+
 source $DGE_HOME/dge_utils.sh
 export PATH=$DGE_HOME:$DGE_HOME/../misc/:$PATH
 
@@ -81,6 +85,10 @@ spin.R $DGE_HOME/dge_analysis.R $baseDir/cuffdiff
 # ... project specific stuff
 screen -R rsync_$project
 
+## main sync
+~/bin/unison $baseDir ssh://bioinfo///home/brandl/mnt/<<MOUNT_PATH>> -fastcheck true -times -perms 0
+
+
 rsync -avsn --delete  $baseDir brandl@fileserver:/projects//file/server/path
 
 mailme "$project: rsync done"