#Processed genome annotation. #Obtained from the ENCODE project. contact: andrea.tanzer@crg.eu #wget http://genome.crg.es/~atanzer/ENCODE/gen10.gtf.gz #wget http://genome.crg.es/~atanzer/ENCODE/gen10.long.gtf.gz #wget http://genome.crg.es/~atanzer/ENCODE/gen10.long.partition.unstr.gtf.gz gen10.gtf.gz: The original GENCODE v10 (ftp://ftp.sanger.ac.uk/pub/gencode/release_10/gencode.v10.annotation.gtf.gz) does not contain tRNAs. I added the entries from a separate gencode v10 file (ftp://ftp.sanger.ac.uk/pub/gencode/release_10/gencode.v10.tRNAs.gtf.gz). For the tRNAs I modified "gene_type" and "transcript_type" attributes and added element "gene" and "transcript". gen10.long.gtf: is a subset and contains only entries of long transcripts (protein coding, processed transcript, pseudogenes, ...) NOTE: the long.gtf file was used for quantification gen10.long.partition.unstr.gtf.gz: Partitioning the genome into elements using the hierarchy gap-exon-intron-intergenic for ~3 billion bg (unstranded). The partition also contain an element called "genic". this partition is loger than exonic+intronic, since transcripts assigned to a gene locus do not necessarily overlap. However, those cases are rather the exception than the rule