README for reproducible stranded CSHL contigs that are either intergenic or antisense to Gencode v19 genes.

Site: http://genome.crg.es/~sdjebali/Gencode/version19/IA_Contigs

Date: Oct 23rd 2014

Contact: sarah.djebali@crg.eu

All CSHL stranded PE RNA-seq experiments with 2 bioreplicates generated until now were considered, i.e. from encode2 + encode 3.

For each of the 106 experiments with 2 bioreplicates, contigs with a npIDR value lesser or equal to 0.1 were retained
and were compared to Gencode v19 genes in a stranded way. The ones that did not overlap a Gencode gene (even by 1 bp)
were considered intergenic or antisense (IA), and were reported in bed format (gzipped) at:
http://genome.crg.es/~sdjebali/Gencode/version19/IA_Contigs/Data
The correspondence between those files and their metadata is available at:
http://genome.crg.es/~sdjebali/Gencode/version19/IA_Contigs/Metadata/index_file_ia_contigs.txt

The stranded projection of the 106 sets of contigs is also reported at:
http://genome.crg.es/~sdjebali/Gencode/version19/IA_Contigs/Data/all_contigs_ia.bed.gz