Sam2Bedgraph.pbs

#!/bin/bash
#PBS -l nodes=1:ppn=1,walltime=3:00:00
#PBS -N Sam2Bedgraph
#PBS -M ${USER}@nyu.edu
#PBS -m abe
#PBS -o localhost:/scratch/${USER}/${PBS_JOBNAME}.o${PBS_JOBID}
#PBS -e localhost:/scratch/${USER}/${PBS_JOBNAME}.o${PBS_JOBID}

module load samtools/intel/1.2
module load bedtools/intel/2.23.0 

# Purpose: to convert a folder of SAM files into bedgraphs
# In this example code, the first folder is assumed be only files mapped to SK1
# and the second folder is assumed to be only filed mapped to SacCer3

cd /scratch/tem298/sk1/

shopt -s nullglob # Avoid expanding to *.sam if there were no .sam files in directory

for f in *.sam
do
  samtools view -h $f > ${f}.bam
  samtools sort $f.bam ${f}.sorted
  samtools index $f.sorted.bam
  samtools view -b $f.sorted.bam | genomeCoverageBed -ibam stdin -bg -g ~/Library/sk1_MvO_V1.chrLen.txt > ${f}.bedgraph
done

cd ../S288C/

shopt -s nullglob # Avoid expanding to *.sam if there were no .sam files in directory

for g in *.sam
do
  samtools view -h ${g} > ${g}.bam
  samtools sort ${g}.bam ${g}.sorted
  samtools index ${g}.sorted.bam
  samtools view -b ${g}.sorted.bam | genomeCoverageBed -ibam stdin -bg -g ~/Library/S288C.chrLen.txt > ${g}.bedgraph
done

exit 0;