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We applied the same approaches to identify homology for our unique transcripts and to identify how many are annotated in the 26,159 HC genes CDS (version: MIPS_23Mar12) [ 21].
RGH DNA sequences including additional 2,000 bp up- and down-stream sequences were extracted from the Gy14 draft genome scaffolds and re-annotated with Augustus (http://bioinf.uni-greifswald.de/augustus/) using 9930 CDS (Version 2.0) [ 26] as reference sequences.
The B1K reads were also mapped onto the filtered chromosomal barley reference genome, Hordeum vulgare 030312 v2.16 from ENSEMBL release 16 and barley HC genes CDS (version: MIPS 23 March 2012) [ 23] using Bowtie-2.
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