title: Sequence_Capture_of_37-48
design: Despite the 3635 Taxon ID, this sequence capture sample contains some reads from diploids related to G. histutum.  See the Sample Names below. 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 independently 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).   Sample Name MID MID Forward Sequence  Coker_315 1  ACGAGTGCGT;  Cascot_L7 2  ACGCTCGACA;  Lkt_511 3  AGACGCACTC;  PM_145 4  AGCACTGTAG;  FM_958 5  ATCAGACACG;  BR_110 6  ATATCGCGAG;  Maxxa 7  CGTGTCTCTA;  D5 8  CTCGCGTGTC;  AD3 9  TAGTATCAGC;  GK 10  TCTCTATGCG;  TAM 11  TGATACGTCT;  A2 12  TACTGAGCTA;