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Strategy Session May 8 2015

- Need to figure out if we need to get more mate-pair data

  1. Are missing data in the fasta files we received
    1. 841k pairs found in files given to us
    2. were told there would be 1M
    3. either something wrong with runs, or library
  2. possibly need a new mp whole library
  3. need to know by next week so have enough time to work with new data


  1. How much does an RNAseq library cost?
    1. Lowe recommends doing small RNAs
  2. Are all expenses/promised expenses listed on the wiki?

- How much does tagmentase and lucigen cost?

  1. how much does the tagmentase library prep cost?
    1. tagmentase likely better quality than lucigen.

- How much tagmentase and lucigen do we need?

- BLAST contigs we have constructed

- Need insert size for Lucigen mate-pair data

- Need contig length distributions from contig assemblies

  1. should make graphs and post to wiki

- Map Lucigen data to current contig assemblies

  1. use BWA or bowtie to map Lucigen to current contigs
  2. need about 1000 pairs of >5000 bp contig lengths
  3. need quick size estimate

- Every group will carry on with their assembler to get contigs

- Need website/ forum to better distribute tasks for assembly

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lecture_notes/05-08-2015.txt · Last modified: 2015/05/08 18:15 by nsaremi