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We then obtained specific reads for each exon 1A and 1B and for constitutive exon 6 as a control.
Independent, experimental validation of primer pairs was necessary for only 2 loci in the 22-loci libraries as they did not show any specific reads for any samples upon sequencing.
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The number of SASI specific reads varies between samples, but for each their representation roughly approximates the 0.1% spike-in level.
a: Specific read counts for E reactions for 24 samples at each of 22 loci.
The assembler includes a novel edge-adjustment algorithm to detect structural defects by examining the neighboring reads of a specific read for sequencing errors and adjusting the edges of the string graph, if necessary.
The assembler includes a novel edge-adjustment algorithm to detect structural defects by examining the neighbouring areas of a specific read for sequencing errors and adjusting the edges of the string graph.
Gene specific read counts for the genes in the high confidence gene set were obtained using the RSEM v. 1.2.12 [ 55], that internally uses bowtie v. 1.0.0 [ 57].
Next generation sequencing of eight, unpooled small RNA libraries derived from milk exosomes produced about 60.5 million high-quality, bovine-specific sequence reads for comparison of miRNA expression between treatments.
b: Specific read counts obtained for E reactions for loci that passed quality control.
The specific read counts obtained for E reactions at each locus clearly clustered into two groups (Fig. 3a).
For each amplicon, we used a Gaussian mixture to model (log 10) specific read count measured for each sample and automatically classify each sample into the high (present) or low (absent) count cluster.
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