Error correction was performed on DNA sequence reads using the QuorUM error correction algorithm [32 ]. After filtering duplicate and low quality reads, 1,622,097,087 unique reads remained. Paired reads were aligned to the UMD3.1 cattle reference assembly using NextGENe 2.4.1 (SoftGenetics, LLC, State College, PA) requiring at least 35 contiguous bases with ≥95.0 % overall match, up to 2 allowable mismatched bases, and up to 100 allowable alignments of equal probability genome-wide.
RNA sequence reads were filtered for quality and adapter sequences and were then trimmed using a custom Perl script already described [31 (link)]. Computations were performed on the HPC resources at the University of Missouri Bioinformatics Consortium (UMBC). TopHat v2.0.6 [33 (link)] was used to map the reads to the Bos taurus UMD3.1 reference genome. A total of 2 mismatches and up to 3 bp indels were allowed in alignment.
RNA sequence reads were filtered for quality and adapter sequences and were then trimmed using a custom Perl script already described [31 (link)]. Computations were performed on the HPC resources at the University of Missouri Bioinformatics Consortium (UMBC). TopHat v2.0.6 [33 (link)] was used to map the reads to the Bos taurus UMD3.1 reference genome. A total of 2 mismatches and up to 3 bp indels were allowed in alignment.