title: Sequence_capture_of_25-36
design: Whole genome DNA samples were extracted using a modified CTAB protocol. Twelve samples were tagged with multiplex identifiers (MIDs), each with a different MID.  They were idependently hybridized to a custom Nimblegen Sequence Capture Array (12-plex).  After washing, the samples were all eluted into a single tube and subjected to ligation-mediated PCR (i.e. PCR using the 454 sequence adapters) to amplify the captured fragments to a high enough concentration for sequencing.  Subsequently, the libraries were prepared for 454 sequencing (size selection on a Capliper XL, emPCR, and bead preparation etc.).  The image files from the sequence were processed with 'less stringent' settings when compared to the default settings for the 454 software pipeline.  Namely, BadFlowThreshold from 4 (default) to 8; LastFlowToTest from 320 (default) to 240; TrimBackScaleFactor 0.7 (default) to 1; errorQscoreWindowTrim from 0.01 (default) to 0.02; QScoreTrimBackScaleFactor from 0.9 (default) to 1.0. The twelve captured samples tagged with multiplex identifiers (MIDs) were run on a single plate (2 large regions) of 454.  The samples were prepared using 'traditional' WGS libraries from Roche.  Below is a list of the samples and MIDs included in this run.  Sample Name MID MID Forward Sequence (in that order). TX_2002 1  ACGAGTGCGT; TX_2090 2  ACGCTCGACA; TX_2091 3  AGACGCACTC; TX_2092 4  AGCACTGTAG; TX_2093 5  ATCAGACACG; TX_2094 6  ATATCGCGAG; TX_2095 7  CGTGTCTCTA; TX_2096 8  CTCGCGTGTC; ARK_2402 9  TAGTATCAGC; ST825 10  TCTCTATGCG; TX_1988 11  TGATACGTCT; DP90 12  TACTGAGCTA;