Project Summaries

09-559  Project Manager: D. C. Jones

SEQUENCING COTTON FIBER ESTS

Joshua A Udall, Brigham Young University

We created repeat-depleted libraries at 1x, 3x, and 6x where 'x' represented the amount of capture-beads containing the probe targets. We sequenced these libraries on BYU's newly acquired Genome Analyzer IIx. We were able to extract partial data from the failed sequencing runs. We trimmed the resulting reads with SICKLE and mapped them to the D5 reference genome sequence using GSNAP (with which we have had great success in mapping cotton reads). We were only able to extract usable data for our 6x-depleted library from the first run and 23,273,206/27,010,720 (86%) reads mapped to the D5 reference. We have now determined that the repeat constitution of D5 is too varied to pull matching sequences from the DNA library with our current technology.

 

Project Year: 2012
 

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