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Non-coding annotations, analyses scripts and resulting manuscript for 48 bird genomes
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data Responding to referee comments. Apr 15, 2014
paper Updated manuscript to address reviewer comments. Aug 7, 2014
scripts Responding to referee comments. Apr 15, 2014
README Amending manuscript, explaining losses, adding more expression data, … Mar 11, 2014

README

bird-genomes
============

Non-coding annotations, analyses scripts and resulting manuscript for 48 bird genomes.

######################################################################
#0. Directories and files:

README      -- this file
data/       -- data directory, primarily genome annotations
  conserved-merged-annotations/
            --Is populated with GFFs generated by gffs2heatmaps.pl. A subset of the "merged-annotations" that are conserved in >10% of the bird genomes. 
  mirbase/  -- miRBase derived annotations in GFF format
  R/        -- data matrices used to generate graphics using R
  RNA-seq/  -- annotations that have been validated using RNA-seq data
  rfam/     -- Rfam derived annotations in GFF format
  trnascan/ -- tRNAscan-SE derived annotations in GFF format
  merged-annotations/
            -- merged annotations from miRBase, Rfam, tRNAscan, ... in GFF format. Generated by the "compete_clans.pl" script
  stadler-annotations/
            -- annotations from Peter Stadler group's set of RNA tools
	    -- fix mis-named chromosomes
paper/      -- files associated with the manuscript (figures/, *.tex, *.bib, ...)
scripts/    -- scripts used for analysing the datasets

######################################################################
#1. annotation tools:

curl ftp://ftp.sanger.ac.uk/pub/databases/Rfam/11.0/database_files/rfam.txt.gz | gunzip > /tmp/rfam.txt &&  cat /tmp/rfam.txt | cut -f 3,4,19 | sort > data/rfam2type.txt

######################################################################
#2. analyses tools:

cd bird-genomes

#Merge all the different annotations, resolve the major overlaps:
# Overlap rules are:
#  1. specific methods (e.g. tRNAscan, miRBase, ...) are selected over Rfam predictions
#  2. High-scoring predictions are selected over low-scoring predictions
#paste all the filenames together (check they coincide if adding new annotations) and run compete_clans.pl:
ls data/rfam/*gff > /tmp/blah1 && 
ls data/trnascan/*gff > /tmp/blah2 && 
ls data/mirbase/*gff > /tmp/blah3 && 
ls data/stadler-annotations/*gff > /tmp/blah4 && 

#CHECK: paste /tmp/blah1 /tmp/blah2 /tmp/blah3 /tmp/blah4 
paste /tmp/blah1 /tmp/blah2 /tmp/blah3 /tmp/blah4 | perl -lane 'if(/mirbase\/(\S+).gff/){print "scripts/compete_clans.pl -g $F[0] -g $F[1] -g $F[2] -g $F[3] -cl data/clan_info.txt -od data/overlaps/ > data/merged-annotations/$1.gff"}' | sh

#generate the count matrices (in data/R) and run the R-code that generates the figures: 
./scripts/gffs2heatmaps.pl


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