lecture_notes:04-03-2015
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lecture_notes:04-03-2015 [2015/04/06 05:00] jennie created |
lecture_notes:04-03-2015 [2015/04/06 17:00] (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}} | ||
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| + | ==== 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: 2015/04/06 05:00 by jennie
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