Commit 01b4dab6 authored by Holger Brandl's avatar Holger Brandl

refined star workflow

parent 342c00c5
...@@ -105,6 +105,10 @@ mcdir $baseDir/alignments ...@@ -105,6 +105,10 @@ mcdir $baseDir/alignments
star_align.kts ${igenome} $(ls ${baseDir}/lanereps_pooled/*.fastq.gz) star_align.kts ${igenome} $(ls ${baseDir}/lanereps_pooled/*.fastq.gz)
dge_bam_correlate . &
mailme "$project: mapping done"
######################################################################################################################## ########################################################################################################################
### Differential Expression Analysis ### Differential Expression Analysis
......
...@@ -127,12 +127,13 @@ evalBash("rm - rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out" ...@@ -127,12 +127,13 @@ evalBash("rm - rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out"
// Do reporting and perform bam correlation (but don't wait for the results) // Do reporting and perform bam correlation (but don't wait for the results)
evalBash(""" evalBash("""
rend.R - e ${'$'}NGS_TOOLS / dge_workflow / star_qc.R. rend.R -e ${'$'}NGS_TOOLS/dge_workflow/star_qc.R .
# Condense counts into matrix # Condense counts into matrix
dge_star_counts2matrix dge_star_counts2matrix
# http://superuser.com/questions/178587/how-do-i-detach-a-process-from-terminal-entirely # http://superuser.com/questions/178587/how-do-i-detach-a-process-from-terminal-entirely
nohup dge_bam_correlate & # disabled since it does not work for functions (see http://stackoverflow.com/questions/16435629/linux-shell-script-call-a-function-by-nohup
#dge_bam_correlate & #nohup dge_bam_correlate . &
#dge_bam_correlate . &
""") """)
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