# format refseq MG1363
bin/prepare-refseqs.pl --fasta docs/MG1363/NC_009004.fna

# add annotation
bin/flatfile-to-json.pl --gff docs/MG1363/NC_009004.gff --trackLabel Original_Annotation --trackType CanvasFeatures
bin/flatfile-to-json.pl --gff docs/MG1363/MG1363_ncRNA_2015Jan.gff --trackLabel smallRNA --trackType CanvasFeatures 

# make link to BAM files in the data/ folder
ln -s /home/anne/PROJECTS/sjoerd/otogenetics_directional/2015Jan_otogenetics sjoerd_2015Jan_otogenetics
ln -s /home/anne/PROJECTS/sjoerd/dRNAseq sjoerd_dRNAseq


# make config file
data/tracks.conf

# If BAM is empty, check the genome header name
/usr/molgentools/tools/find_and_replace_single.pl -i MG1363_A.sorted.bam -f 'gi|125622882|ref|NC_009004.1|' -r 'NC_009004.1' -o MG1363_A.sorted.new.bam


# make feature searchable
bin/prepare-refseqs.pl -gff docs/MG1363/MG1363_ncRNA_2015Jan.gff
bin/generate-names.pl 

# Add tracks to data/tracks.conf

# BAM to BigWig


samtools sort control_A_F.bam control_A_F.sorted
bamToBed -i control_A_F.sorted.bam > control_A_F.sorted.bed

genomeCoverageBed -bg -ibam control_A_F.sorted.bam -g chromsizes.txt > control_A_F.bedgraph
genomeCoverageBed -bg -ibam control_A_F.sorted.bam -g chromsizes.txt -strand + > control_A_F.plus.coverage
genomeCoverageBed -bg -ibam control_A_F.sorted.bam -g chromsizes.txt -strand - > control_A_F.minus.coverage

bedGraphToBigWig control_A_F.bedgraph chromsizes.txt control_A_F.bw
bedGraphToBigWig control_A_F.plus.coverage chromsizes.txt control_A_F.plus.bw
bedGraphToBigWig control_A_F.minus.coverage chromsizes.txt control_A_F.minus.bw

genomeCoverageBed -bg -ibam eurofins_B_TEX.sorted.bam -g chromsizes.txt > eurofins_B_TEX.bedgraph
genomeCoverageBed -bg -ibam eurofins_B_TEX.sorted.bam -g chromsizes.txt -strand + > eurofins_B_TEX.plus.coverage
genomeCoverageBed -bg -ibam eurofins_B_TEX.sorted.bam -g chromsizes.txt -strand - > eurofins_B_TEX.minus.coverage

bedGraphToBigWig eurofins_B_TEX.bedgraph chromsizes.txt eurofins_B_TEX.bw
bedGraphToBigWig eurofins_B_TEX.plus.coverage chromsizes.txt eurofins_B_TEX.plus.bw
bedGraphToBigWig eurofins_B_TEX.minus.coverage chromsizes.txt eurofins_B_TEX.minus.bw