Athurva Gore/LabNotes/2010-3-24: Difference between revisions
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=IPS Mutation Paper= | =IPS Mutation Paper= | ||
==Indel Calling== | ==Indel Calling== | ||
===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"