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In a recent paper RNA editing in the human ENCODE RNA-seq data, reads were aligned to human reference (GRCv37 / UCSC hg19) plus GENCODE v7 splice junctions and added spike sequences.
I've downloaded the GENCODE v7 annotation gtf file. Is it correct to assume the splice junctions in the gtf file are the same as the ones in the paper e.g. I used gtf_junc to create a junc file for tophat I then specified the with with -j in tophat from there tophat creates the bowtie indexes segment_junc.*.ebwt and the segment_junc.rev.*.ebwt. Can I assume this bowtie index to be the GENCODE v7 splice junctions?
I've downloaded the GENCODE v7 annotation gtf file. Is it correct to assume the splice junctions in the gtf file are the same as the ones in the paper e.g. I used gtf_junc to create a junc file for tophat I then specified the with with -j in tophat from there tophat creates the bowtie indexes segment_junc.*.ebwt and the segment_junc.rev.*.ebwt. Can I assume this bowtie index to be the GENCODE v7 splice junctions?