MACS

HPC Server log in and init

scp 111@auhpc-headnode.augusta.edu:temp/*.* ./
scp *.* 111@@auhpc-headnode.augusta.edu:

ssh campus_account@auhpc-headnode.augusta.edu
module initadd sge/2011.11p1
module initadd openmpi/open64/64/1.10.1
module add tophat/2.1.1 
module add bowtie2/2.2.6 

HPC Server commandline

echo 'tophat2 command_lines…' | qsub -l hostname=auhpc013 -V -cwd -j y -o tophat2.log -N tophat2.test

echo 'R CMD BATCH test.R'| qsub -l hostname=auhpc013 -V -cwd -j y -o testR.log -N R.test

tail -f *.log

MACS2

# --format=BAMPE : paired read
callpeak --format=BAMPE -c Input.bam -B --SPMR -t Control.bam -n OutputDir -g hs

# -g/--gsiz hs : 2.7e9
callpeak --format=BAM -c Input.bam -B --SPMR -t Control.bam -n OutputDir -g hs

BWA VN:0.7.10-r789

bwa sampe -P -n 100 -a 500 -o 3 -r Input.fastq.1 Input.fastq.2

reference

https://github.com/taoliu/MACS