mtw

#!/bin/bash

cutadapt=`which cutadapt`
fastqc=`which fastqc`
bam2fastq=`which bam2fastq`
gzip=`which gzip`
origdir="."
results="cutadapt"
fastqcdir="${results}/FastQC"
adapter5="AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"

mtw

#!/bin/bash
chromsizes="./chrom.sizes"
genomeCoverageBed=`which genomeCoverageBed`
bedGraphToBigWig=`which bedGraphToBigWig`
vis="./vis"
samples=9
fromsample=1
rep=2
fromrep=1

mtw

cat ORIG.gff | perl -ne 'chomp; if($_ =~ /^\#/){print $_."\n";next;} my @F = split("\t"); if ($F[6] eq "+"){$F[6] = "-"}else{$F[6] = "+"};my $part1 = join("\t",$F[0],$F[1],$F[2],$F[3],$F[4],$F[5],$F[6],$F[7],$F[8]);print $part1."\n"' > ! AS.gff

mtw

#!/bin/bash

fastqcdir="./FastQC"

if [ -d "$fastqcdir" ];
then
        echo "$fastqcdir available"
else
        mkdir $fastqcdir
fi

mtw

#!/bin/bash
countdir="./count"
count_mapped_reads=`which count_mapped_reads_fast.pl`
bam_stat=`which bam_stat.py`
samtools=`which samtools`
samstats=`which sam-stats`

if [ -d "$countdir" ];
then
echo "$countdir available"

mtw

#!/bin/bash

segemehl="/scratch/mtw/src/segemehl-svn/segemehl/segemehl.x"
results="./alignments"
reffa="../../genomes/TAIR10/TAIR10.fa"
refidx="../../genomes/TAIR10/TAIR10.idx"
samples=2
rep=3

if [ -d "$results" ];

mtw

#!/bin/bash
# generate coverage profiles
vis="./vis"
chromsizes="foo.chrom.sizes"
genomeCoverageBed=`which genomeCoverageBed`
bedGraphToBigWig=`which bedGraphToBigWig`

if ! [ -d "$vis" ];
then
mkdir -p $vis

mtw

#!/bin/bash
samdir="./"
annotation="my.gtf"
htseqdir="./htseq-count"
htseqcount=`which htseq-count`
samtools=`which samtools`
feature="gene"
idattr="gene_name"
ss="reverse"

mtw

#!/bin/bash

cutadapt=`which cutadapt`
fastqc=`which fastqc`
origdir=".."
results="."
fastqcdir="${results}/FastQC"
adapter5="CTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
adapter3="GATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
inprefix="C"

mtw

#!/bin/bash
samdir="./"
dexseq_flat_gff="my.DEXSeq.gff"
outdir="./dexseq-count"
dexseq_count="python /home/foo/bin/dexseq_count.py"
samtools=`which samtools`

if ! [ -d "$outdir" ];
then
        mkdir -p $outdir