Matt:LabNotes/2015-5-14: Difference between revisions

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>Mzcai
(Created page with "==Regression Analysis of CA12kNov2014 V4 probeset + 100x suppressor== *Files in Dropbox/GradZhangLab/CA12k_Nov2014/V4_CaptureAnalysis/20150514/ *DARTFISH counts from Summary2...")
 
>Mzcai
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===DARTFISH vs BAs and HBRR===
===DARTFISH vs BAs and HBRR===
*DARTFISH counts normalized by gDNA counts
*DARTFISH counts normalized by gDNA counts
**Despite DARTFISH being from BA8 it is the worst correlation...
[[File:DARTFISHgNorm_vs_BA8.png|450px]]
[[File:DARTFISHgNorm_vs_BA8.png|450px]]
[[File:DARTFISHgNorm_vs_BA10.png|450px]]
[[File:DARTFISHgNorm_vs_BA10.png|450px]]

Revision as of 03:07, 16 May 2015

Regression Analysis of CA12kNov2014 V4 probeset + 100x suppressor

  • Files in Dropbox/GradZhangLab/CA12k_Nov2014/V4_CaptureAnalysis/20150514/
  • DARTFISH counts from Summary2_S1_V4_Supp_2015-05-06_Try1.txt
    • 18 Positions of V4 in BA8 using first generation of 100x suppressor oligos for CA12kNov2014 probeset
  • Brain Tissue RNA-Seq FPKM Data:
 /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/
  • Files moved to Dropbox/GradZhangLab/CA12k_Nov2014/V4_CaptureAnalysis/
    • eg. RL-BA8-sec9-t-N701-15May14_S1_mapped_genes.fpkm_tracking.txt
    • BA8, BA10, BA17, BA21, BA22, BA41

Normalize in vitro Capture and check with RNA-Seq

  • Captured cDNA from HBRR
  • Normalize with gDNA counts
  • Compare to HBRR FPKM values

File:CDNA vs HBRR.png

  • Better than comparing with BA8 (as expected)
    • Some correlation also expected since HBRR is from all areas of brain and many samples

File:CDNA vs BA8.png

DARTFISH vs BAs and HBRR

  • DARTFISH counts normalized by gDNA counts
    • Despite DARTFISH being from BA8 it is the worst correlation...

File:DARTFISHgNorm vs BA8.png File:DARTFISHgNorm vs BA10.png File:DARTFISHgNorm vs BA17.png File:DARTFISHgNorm vs BA21.png File:DARTFISHgNorm vs BA22.png File:DARTFISHgNorm vs BA41.png

  • HBRR has best correlation
    • Is this due to BA sequencing by Smart-Seq bias?

File:DARTFISHgNorm vs HBRR.png