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Nested primers for amplification of bisulfite converted DNA (Additional file 13) were designed using MethPrimer [ 89] and the sequencing data analyzed using BiQ analyzer [ 90].
DMEAS offers user-friendly interfaces for researchers to import the high-throughput methylation sequencing data analyzed with Bismark software (Krueger and Andrews, 2011).
For both the simulated and cell line data sets, the sequencing data analyzed is sampled from genomic regions on a gene-size scale (i.e. tens or hundreds of kbp).
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The 16S rDNA region was amplified, MiSeq was performed and sequence data analyzed.
The high-resolution sequence data analyzed in this study reveals previously hidden diversity within the Native American mtDNA gene pool.
The aligned sequence data analyzed in this study are available as supporting Text S3, S4, S5, S6, S7, S8, S9, and Text S10.
The DNA sequence data analyzed in this study are available on the NCBI Sequence Read Archive (SRA Accession Number SRA045862).
Gene prioritization strategies that utilize sequence data analyzed by the common reference approach will fail to identify these variants.
This discrepancy observed in different studies may be accounted to (i) amount of sequence data analyzed, (ii) criteria for SSR identification, and (iii) different sources of derived sequences.
For analyses allowing for missing data the full range of read lengths among individuals was used, increasing the amount of sequence data analyzed.
Indeed, as I noted above, it appears to be quite useful for modelling the intron sequence data analyzed in the article.
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