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A comparison of our genetic map results to the genome assembly allowed us to place three knobs on the B73 genome assembly (K4L2, K5L, and K9S).
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Cufflinks v2.0.2 [ 35] (parameters: -F 0) was employed to assemble poly(A)+ RNA-seq mapping results to obtain de novo RNA transcripts.
We extended the previous mapping results to the intraspecific level by testing the hypothesis that E24C3 is linked to the sex-determining factor in the species A. mexicanum.
PoPoolation typically requires DNA from pooled samples from multiple individuals; it then uses the read mapping results to estimate population wide frequencies.
We mapped the sequencing reads, known plant miRNA mature sequences and hairpin sequences from miRBase (Release18) to B. rapa genome sequences (v1.1), then merged the 3 mapping results to identify the conserved miRNA loci.
The SAM tools package [ 30] was used to convert mapping results to BAM format, and then the Picard program (http://picard.sourceforge.net) was applied to eliminate duplicated reads generated during the process of library construction.
It aligns RNA-Seq reads to reference genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
By comparing our QTL mapping results to those from previous studies in sunflower, we have further documented the existence of numerous apparent parallels in the genetic architecture of domestication-related traits within the Compositae.
Transcript quantification : Grape uses the mapping results to produce quantifications of the abundance of a number of transcribed elements: exons, splice junctions, genes and transcripts, as well as inclusion indices for exons.
CONTIGuator [ 9] was used to map resulting contigs to the reference genome 0140J for comparative analysis of genomic regions.
After normalizing to the population template, the registration algorithms of SPM5 were used to map our results to the pediatric CCHMC2 template.
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