updating statanal

diff_exp/geneabundance.sh

@@ -42,5 +42,5 @@ module load subread/1.6.1 stringtie/1.3.2d-intel
 featureCounts -s $stranded -M --fraction -J --ignoreDup -T $SLURM_CPUS_ON_NODE -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
 mkdir ${pair_id}_stringtie
 cd ${pair_id}_stringtie
-stringtie ../${sbam} -p $SLURM_CPUS_ON_NODE -G ../${gtf} -B -e -o denovo.gtf -A ../${pair_id}.fpkm.txt
+stringtie ../${sbam} -p $SLURM_CPUS_ON_NODE -G ${gtf} -B -e -o denovo.gtf -A ../${pair_id}.fpkm.txt
  

genect_rnaseq/concat_ctsum.pl

+#!/usr/bin/perl -w
+#merge_tables.pl
+
+use Getopt::Long qw(:config no_ignore_case no_auto_abbrev);
+use File::Basename;
+
+my %opt = ();
+my $results = GetOptions (\%opt,'outdir|o=s','help|h');
+
+$opt{outdir} = './' unless ($opt{outdir});
+
+my @files = @ARGV;
+foreach $file (@files) {
+    chomp($file);
+    open IN, "<$file" or die $!;
+    $fname = basename($file);
+    my $sample = (split(/\./,$fname))[0];
+    $samps{$sample} = 1;
+    my $head = <IN>;
+    chomp($head);
+    my @colnames = split(/\t/,$head);
+    while (my $line = <IN>) {
+	chomp($line);
+	my @row = split(/\t/,$line);
+	my $gene = $row[0];
+	my $ct = $row[-1];
+	$cts{$gene}{$sample} = $ct;
+    }
+    close IN;
+}
+
+open OUT, ">$opt{outdir}\/countFeature.txt" or die $!;
+my @samples = sort {$a cmp $b} keys %samps;
+print OUT join("\t",'FeatureCtType',@samples),"\n";
+foreach $gene (keys %cts) {
+    my @line;
+    foreach $sample (@samples) {
+	unless ($cts{$gene}{$sample}) {
+	    $cts{$gene}{$sample} = 0;
+	}
+	push @line, $cts{$gene}{$sample};
+    }
+    print OUT join("\t",$gene,@line),"\n";
+}
+close OUT;

genect_rnaseq/statanal.sh

+#!/bin/bash
+#rnaseqalign.sh
+
+usage() {
+  echo "-h Help documentation for hisat.sh"
+  echo "-d  --DEA"
+  echo "Example: bash statanal.sh"
+  exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :d:h opt
+do
+    case $opt in
+        d) dea=$OPTARG;;
+        h) usage;;
+    esac
+done
+
+shift $(($OPTIND -1))
+
+# Check for mandatory options
+if [[ -z $SLURM_CPUS_ON_NODE ]]
+then
+    SLURM_CPUS_ON_NODE=1
+fi
+source /etc/profile.d/modules.sh
+
+perl $baseDir/scripts/concat_cts.pl -o ./ *.cts
+perl $baseDir/scripts/concat_fpkm.pl -o ./ *.fpkm.txt
+perl $baseDir/scripts/concat_ctsum.pl -o ./ *.cts.summary
+cp design.txt design.shiny.txt
+cp geneset.gmt geneset.shiny.gmt
+
+if [[ $dea == 'skip' ]]
+then
+    touch empty.png
+    touch bg.rda
+else
+    module load R/3.2.1-intel
+    Rscript  $baseDir/scripts/dea.R
+    Rscript $baseDir/scripts/build_ballgown.R *_stringtie
+    perl $baseDir/scripts/concat_edgeR.pl *.edgeR.txt
+fi