Author: Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga
Title: Capturing diverse microbial sequence with comprehensive and scalable probe design Document date: 2018_3_12
ID: a9lkhayg_89
Snippet: For our comparison of within-sample variant frequencies with and without capture (Fig. 3d, Supplementary Table 6 ), we used 3 dengue virus samples (DENV-SM1, DENV-SM2, and DENV-SM5). We selected these because of their relatively high depth of coverage, in both pre-and post-capture genomes (Supplementary Table 3 ); the high depth in precapture genomes was necessary for the comparison. We did not subsample reads prior to this comparison, in order .....
Document: For our comparison of within-sample variant frequencies with and without capture (Fig. 3d, Supplementary Table 6 ), we used 3 dengue virus samples (DENV-SM1, DENV-SM2, and DENV-SM5). We selected these because of their relatively high depth of coverage, in both pre-and post-capture genomes (Supplementary Table 3 ); the high depth in precapture genomes was necessary for the comparison. We did not subsample reads prior to this comparison, in order to maximize coverage for detection of rare variants. For each of the three samples, we pooled data from three sequencing replicates of the same pre-capture library prior to downstream analysis. For each of these samples we performed two capture replicates on the same pre-captured library (two replicates with V WAFR and two with V ALL ), and sequenced, estimated, and plotted frequencies separately on these replicates.
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