how to install MACS, STRINGTIE and GFFCOMPARE

wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz

tar -zxvf MACS-1.4.2-1.tar.gz

python setup.py install --prefix /users/rg/gbogu/software/MACS-1.4.2

export PYTHONPATH=/users/rg/gbogu/software/MACS-1.4.2/lib/python2.7/site-packages/:$PYTHONPATH

export PATH="/users/rg/gbogu/software/MACS-1.4.2/bin/:$PATH"

# Also add to ~/.bashrc file

export PYTHONPATH=/users/rg/gbogu/software/MACS-1.4.2/lib/python2.7/site-packages/:$PYTHONPATH

export PATH="/users/rg/gbogu/software/MACS-1.4.2/bin/:$PATH"

# now run

macs14

# also need Peak Splitter software to run this MACS

wget http://www.ebi.ac.uk/sites/ebi.ac.uk/files/groups/bertone/software/PeakSplitter_Cpp_1.0.tar.gz

tar -zxvf PeakSplitter_Cpp_1.0.tar.gz

export PATH=/users/rg/gbogu/software/PeakSplitter_Cpp/PeakSplitter_Linux64/:$PATH

# usage examples:

# macs14 <-t tfile> [-n name] [-g genomesize] [options]

macs14 -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks
 
# pwd
# time
# tissue:EBV

# macs14 -t /nfs/no_backup/rg/projects/GTEx/download/work/b5/9ee0f5b1c1e29bf9a9584634f27f58/SRR1071403.bam -f BAM -g hs -n 1st_20files_EBV -w --call-subpeaks

# /users/rg/gbogu/software/stringtie-1.0.4.Linux_x86_64/stringtie /nfs/no_backup/rg/projects/GTEx/download/work/b5/9ee0f5b1c1e29bf9a9584634f27f58/SRR1071403.bam -o SRR107140_denovo_transcripts.gtf
awk '{print "chr"$0}' SRR1071403.denovo.transcripts.gtf | grep -v "#" |grep -v random |grep -v chrM |grep -v chrUn |grep -v _hap |grep -v chrNC | grep -v chrGL| sort > S
rm SRR1071403.denovo.transcripts.gtf
mv S SRR1071403.denovo.transcripts.gtf


wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.9.8.Linux_x86_64.tar.gz
tar -zxvf gffcompare-0.9.8.Linux_x86_64.tar.gz
cd /users/rg/gbogu/software/gffcompare-0.9.8.Linux_x86_64

Removing false poistives (expressed and intergenic repeats)

https://cloud.githubusercontent.com/assets/3885659/20972771/45e20bb4-bc96-11e6-8501-2c61310efc41.jpg