Sequence Lengths

http://eagle.fish.washington.edu/cnidarian/TJGR_oyster_v9_scaff_length.txt



---
cg


http://eagle.fish.washington.edu/cnidarian/oyster_v9_CG_fuzznuc.output



NEED BED or GFF 

http://eagle.fish.washington.edu/cnidarian/TJGR_oyster_v9_CG.gff



robertsmac:~ sr320$ grep -c " + pattern: CG" /Volumes/web/cnidarian/oyster_v9_CG_fuzznuc.output
9978551




./intersectBed -a /Volumes/AquaculX/armina/oyster.v9.glean.final.rename.CDS.gff -b /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff -c > /Volumes/web/cnidarian/TJGR_intersectbed_CDS_v9_CGmotif.txt 

http://eagle.fish.washington.edu/cnidarian/TJGR_intersectbed_CDS_v9_CGmotif.txt


./intersectBed -a /Volumes/AquaculX/armina/oyster.v9.glean.final.rename.mRNA.gff -b /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff -c > /Volumes/web/cnidarian/TJGR_intersectbed_mRNA_v9_CGmotif.txt 

http://eagle.fish.washington.edu/cnidarian/TJGR_intersectbed_mRNA_v9_CGmotif.txt



?promoter

./intersectBed -a /Volumes/web/cnidarian/TJGR_genes_v9_promoter_5p1000.gff -b /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff -c > /Volumes/web/cnidarian/TJGR_intersectbed_promoter_v9_CGmotif.txt 




Repeats

./intersectBed -a  /Volumes/web/cnidarian/Repeat_oyster.v9.fa.out.gff -b /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff -c > /Volumes/web/cnidarian/TJGR_intersectbed_Repeat_v9_CGmotif.txt 

http://eagle.fish.washington.edu/cnidarian/TJGR_intersectbed_Repeat_v9_CGmotif.txt