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Our work, which focused on mapping to individual LTR-RT elements, identified distinct patterns of sRNA targeting within sugarcane LTR-RT lineages and families.
We wrote a tool, novoPile (available at http://www.gene.cimr.cam.ac.uk/todd/) to generate a 'pileup' file of bases mapping to individual reference sequence positions directly from the novoalign output.
Coverage of the genome for construction of a deletion bin map can be conservatively estimated by the number of probes mapping to individual deletion bins.
HTSeq (0.5.3p3,) was used to perform gene counting while BEDTools (2.7.1) [ 18] was used to count the reads mapping to individual exons.
The coverageBed script from BEDTools was used to count reads mapping to individual exons in the RefSeq database (see Additional file 1).
We constructed a set of MAPH probes consisting of test probes mapping to individual beta-defensin genes and reference probes that have been shown to be non-variable in copy number [ 43].
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To count reads mapped to individual genes in Gencode, the program featureCounts [ 16] was used.
The maps will show where crimes have been committed, with some types of crime mapped to individual streets, and allow citizens to compare their neighbourhood with others and hold their police to account.
The HvGSL genes, designated HvGSL2 to HvGSL7, were mapped to individual loci that were distributed across the barley genome on chromosomes 3H, 4H, 6H and 7H.
"The number is of course opaque but offers some indicator of sell-through for the game, as it is mapped to individual Microsoft Xbox Live and Sony PlayStation Network accounts," said Piers heading-Rofls, head of games at IHS Technology.
Before an abstract specification can be translated into an efficient implementation in software and hardware, the dataflow networks need to be partitioned and then mapped to individual processing elements.
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