Athurva Gore/LabNotes/2010-3-24

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Plan for Today[edit]

  • Indel calling - run scripts
    • CV-iF/CV-F and DF6/FS Exome data
    • Nimblegen data (whatever is available)
  • BSPP Neural Network
    • Assemble Cpg97k data, BS_FirstExon data; see how this NN looks

IPS Mutation Paper[edit]

Indel Calling[edit]

Data to assemble[edit]

Flowcell CV-F CV-iF DF6 FS
HL020 s3, s4 s1, s2
HL022 s1, s2 s3, s4
HL023 s5, s6 s7, s8
HL025 s6 s7
HL026 s1 s5 s6 s7
HL036 s1 (NimbleGen) s4 (NimbleGen)
HL037 s3 (NimbleGen) s8 (NimbleGen)

Procedure[edit]

  • Merged CV-iF, CV-F, DF6, and FS
    • Running mapping+velvet script on CV-iF and CV-F
  • Still need to merge NimbleGen data

CNV-Seq[edit]

  • Can we use Exome data to find CNV variation?
    • Theoretically, bias in probeset should be uniform
    • May not be true in practice
  • Once CV-F and CV-iF data is finished sorting (should be a couple hours), try CNV algorithm on it
    • See what results we get
  • Perhaps rather than trying to compare windows, we should compare the number of reads that map to each exon...
    • Variable size, can we model it properly?

BSPP Neural Network[edit]