co-anno

Author:	Gina Turco (gturco), Brent Pedersen (brentp)
Email:	gturco88@gmail.com
License:	MIT

Contents

• co-anno
• Description
• Installation
• Run
  • Inputs
    • Editing Run File
    • Output files

Description

Coding sequences of one species are blast to the noncoding sequences of the other. Blastn is ran at a word size of 20 and E-Value < 0.001. Blast hits that hit the same coding region are summed by length. Groups with a sum greater then 100 are recorded as a missed exon strand.

Installation

• Python version >= 2.7
• blast (download latest and run)
• lastz (download latest .tar.gz; configure; make; make install) and adjust path in quota.sh)
• bpbio (svn checkout http://bpbio.googlecode.com/svn/trunk/ bpbio-read-only) (run biostuff,coanno and bblast sudo python setup.py install)

Run

Inputs

• Fasta File (it is recommended to run 50x mask repeat)
• Bed File (supports UCSC bed format)
• Converting GFF to Bed

BCBio module required:

python scripts/gff_to_bed.py rice_v6.gff >rice_v6.bed

• If you have access to Coge the fasta and bed file for each organism can be obtained using export_to_bed.pl e.g.:

  perl scripts/export_to_bed.pl \
                        -fasta_name rice_v6.fasta \
                        -dsg 8163 \
                        -name_re "^Os\d\dg\d{5}$" > rice_v6.bed
  

  where dsg is from CoGe OrganismView and the prefix for the .bed and .fasta file must be the same (in this case rice_v6). You likely need to run this on new synteny and then copy the .bed and .fasta files to the data/ directory. The -name_re regular expression is not required, but in this case, it will prefer the readable Os01g101010 names over the names like m103430.

Editing Run File

• Once only: edit quota.sh to correct path for quota-alignment
• edit quota.sh to the correct ORGA, ORGB, QUOTA
• run cmd: sh run.sh #that will call quota.sh (this will take a long time as it's doing a full blast (lastz) and then all of quota align, then cns pipeline).
• this will create png's for the dotplots. check those to make sure the quota-blocks look correct.

Output files

• Query and subject CNS position
• Missing Exons from ORGA ORGB blast
• CNS blast to RNA file
• CNS blast to proteins file
• CNS assigned to nearest Ortholog