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gencode.v16.annotation.gtf is the original ENCODE gtf file and can be obtained here: ftp://ftp.sanger.ac.uk/pub/gencode/release_16/gencode.v16.annotation.gtf.gz I used make-tables.R to extract the transcripts and genes and make two new gtf files. gencode.v16.annotation.genes.gtf.gz gencode.v16.annotation.transcripts.gtf.gz These tables are subsets of the original except for these addition to the attribute column: 1- the first addition is a unique ID (feature_id) 2- the second addition is the row number of the original file corresponding to the entry (original_row) 3- rows were appended to the end to annotate the ENCODE spikeins Note that the files exon.id.txt, genes.id.txt and transcript.id.txt contain just the feature_ids You can use the file sanitycheck.R to check if the tables columns and rows match An example submission is here: exampleSubmission.tgz Note 1: that there is also an exon table: gencode.v16.annotation.exon.gtf.gz in case we want to permit future exon submissions Note 2: the files spikein_exon.gtf, spikein_gene.gtf, spikein_transcript.gtf contain just the spike-ins. These have been appended to the end of the annotation files
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