#Run bamCorrelate to exclude replicates:
#This tool is useful to assess the overall similarity of different BAM files. A typical application is to check the correlation between replicates or published data #sets.The tool splits the genomes into bins of given length. For each bin (100b), the number of reads found in each BAM file is counted and a correlation (Spearman) is computed for all pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples.

giagkas@fix:/data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k$ bamCorrelate bins --binSize 100 --bamfiles IL4-15mMm.bam.md.bam IFN-15mMm.bam.md.bam 0hrep1-15mMm1kIntron.bam.md.bam 0hrep2-15mMm.bam.md.bam 0hrep3-15mMm1kIntron.bam.md.bam 2hrep1-15mMm1kIntron.bam.md.bam 2hrep2-15mMm1kIntron.bam.md.bam 2hrep3-15mMm1kIntron.bam.md.bam 6hrep1-15mMm.bam.md.bam 6hrep2-15mMm.bam.md.bam 6hrep3-15mMm1kIntron.bam.md.bam --labels IL4 IFN 0hrep1 0hrep2 0hrep3 2hrep1 2hrep2 2hrep3 6hrep1 6hrep2 6hrep3 --corMethod spearman -o ~/giagkas/corspearman.pdf
Number of non zero bins found: 2350202
/usr/lib/python2.7/dist-packages/matplotlib/collections.py:571: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'): 

file:///home/giagkas/giagkas/parclip/1kIntron/coverage/corspearman.pdf 

#create Big Wig files:
file:///home/giagkas/giagkas/parclip/1kIntron/bamcoverage_v1.sh
giagkas@fix:~/giagkas/parclip/1kIntron$ ./bamcoverage_v1.sh