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lecture_notes:04-03-2015

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lecture_notes:04-03-2015 [2015/04/05 22:00]
jennie created
lecture_notes:04-03-2015 [2015/04/06 10:00] (current)
sihussai
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 **Guest Lecturer: ​ Steven Weber**\\ **Guest Lecturer: ​ Steven Weber**\\
 Full Presentation:​ {{lecture_notes:​slug_presentation.pdf}} Full Presentation:​ {{lecture_notes:​slug_presentation.pdf}}
 +
 +==== General Notes ====
 +  - Administrative:​ read about your [[teams: | team'​s]] assigned assembler. ​
 +  - Our data is from one wild-caught slug (//​Ariolimax dolichophallus//​). ​
 +  - Library prep is not a nice clean process, every possible weird thing that can happen with the DNA pretty much does. 
 +  - What data do we have? 
 +    - Full lane of larger insert library on Miseq (2x300 bp, ~26M reads)
 +    - Full Hiseq lanes of each library (2x100 bp, ~150M reads each)
 +    - Mate pair library has been sequenced, need an assembly of shotgun data first (to map the mate pair reads onto) to determine quality of mate pair library reads. ​
  
 ==== A. Dissection ==== ==== A. Dissection ====
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 ==== D. Lucigen Nxseq Long Mate Pair Library Prep ==== ==== D. Lucigen Nxseq Long Mate Pair Library Prep ====
  
-Followed instructions exactly, with the exception of manually size selecting on 0.75% Agarose field inversion gel instead of selecting using AMPure beads+  - Followed instructions exactly, with the exception of manually size selecting on 0.75% Agarose field inversion gel instead of selecting using AMPure beads 
 +  - Mate pair library: essentially use a long insert size, but remove the middle so that Illumina can handle the sequencing. This helps with placing contigs together. ([[http://​www.illumina.com/​technology/​next-generation-sequencing/​mate-pair-sequencing_assay.html | more info]]) ​
lecture_notes/04-03-2015.1428296426.txt.gz · Last modified: 2015/04/05 22:00 by jennie