added more qc tools

chipseq_workflow/cs_snippets.sh

@@ -66,6 +66,8 @@ mcdir $baseDir/qc_phantompeaks
 ctrlBam=$baseDir/alignments_untrimmed/H3-3_Rep1_Lane1_Lib4453.bam
 #DEBUG ctrlBam=$baseDir/alignments_untrimmed/H3K4me3_Rep2_Lane2_Lib4455.bam
 
+
+Rscript /projects/bioinfo/holger/bin/phantompeakqualtools/run_spp.R
 for bamFile in $baseDir/alignments_untrimmed/*bam ; do
     echo "processing $bamFile..."
 #    Rscript /home/brandl/bin/phantompeakqualtools/run_spp.R -c=$bamFile -savp -ou  t=$(basename $bamFile).pt.log