Exons from UCSC hg19_knowngene
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7.4 years ago
soloway ▴ 10

I'm trying to create a bed file with all known exons from HG19 in a separate row, with chr#, exon boundaries, strandedness and gene identifier also in each row.

In UCSC, there are many table schema with the necessary info, including exon boundaries listed in fields. But there is often more than one exon in a row, all in a single column, with each exon's boundaries separated by a comma in 'longblob' format. I'm at a loss for the linux commands that will enable me to perform the necessary operations on the longblob entries to create the bedfile I need.

Any advice?

gene • 1.3k views
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