Athurva Gore/LabNotes/2010-3-24: Difference between revisions

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>Ajgore
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=IPS Mutation Paper=
=IPS Mutation Paper=
==Indel Calling==
==Indel Calling==
* Data to assemble:
===Data to assemble===
{| {{table border="1" cellpadding="4" cellspacing="0" style="border:\#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"}}
{| {{table border="1" cellpadding="4" cellspacing="0" style="border:\#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"}}
| align="center" style="background:#f0f0f0;"|'''Flowcell'''
| align="center" style="background:#f0f0f0;"|'''Flowcell'''
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| HL037||||||s3 (NimbleGen)||s8 (NimbleGen)
| HL037||||||s3 (NimbleGen)||s8 (NimbleGen)
|}
|}
===Procedure===
* Currently merging CV-F and CV-iF data using "gunzip -c"


=BSPP Neural Network=
=BSPP Neural Network=

Revision as of 19:13, 24 March 2010

Plan for Today

  • 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

Indel Calling

Data to assemble

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

  • Currently merging CV-F and CV-iF data using "gunzip -c"

BSPP Neural Network