Kun:LabNotes/MONOD/2014-3-18: Difference between revisions

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==MONOD Round 3==
==MONOD Round 3==
===Target identification===
*The specificity of the Round 2 probe set seemed to be very low. Dinh found that 42.5% of the captured targets overlap with repeats. This could explain many off-target reads.  
*The specificity of the Round 2 probe set seemed to be very low. Dinh found that 42.5% of the captured targets overlap with repeats. This could explain many off-target reads.  
*In this re-design, I included the RRBS data (ENCODE, GSE52140) for the A549 and HTB56 lung cancer cell line for identifying cancer DMS. In addition, I also added ENCODE RRBS data from normal brain, lung and pancreas as the controls.   
*In this re-design, I included the RRBS data (ENCODE, GSE52140) for the A549 and HTB56 lung cancer cell line for identifying cancer DMS. In addition, I also added ENCODE RRBS data from normal brain, lung and pancreas as the controls.   
   ./[[Media:find_DMS_PANC_GBM_LC_v3.txt|find_DMS_PANC_GBM_LC_v3.pl]] > GBM_PC_LC_DMS_v3.txt
   ./[[Media:find_DMS_PANC_GBM_LC_v3.txt|find_DMS_PANC_GBM_LC_v3.pl]] > GBM_PC_LC_DMS_v3.txt
   ../extract_clusters.pl GBM_PC_LC_DMS_v3.txt > [[Media:GBM_PC_LC_DMS_clusters.v3.txt|GBM_PC_LC_DMS_clusters.v3.txt]]
   ../extract_clusters.pl GBM_PC_LC_DMS_v3.txt > [[Media:GBM_PC_LC_DMS_clusters.v3.txt|GBM_PC_LC_DMS_clusters.v3.txt]]
===Probe design===
*I pretty much followed the same design as the MONOD Round 2 probes.
*Input files: [[Media:GBM_PC_LC_DMS_clusters_v3_input_plus.txt|GBM_PC_LC_DMS_clusters_v3_input_plus.txt]];[[Media:GBM_PC_LC_DMS_clusters_v3_input_minus.txt|GBM_PC_LC_DMS_clusters_v3_input_minus.txt]]
*Job files:[[Media:jobFile_GBM_PC_LC_DMR_150_plus.txt|jobFile_GBM_PC_LC_DMR_150_plus.pl]];[[Media:jobFile_GBM_PC_LC_DMR_150_minus.txt|jobFile_GBM_PC_LC_DMR_150_minus.pl]]
*ppDesigner output: [[Media:GBM_PC_LC_DMS_probes_v3.txt|GBM_PC_LC_DMS_probes_v3.txt]]

Revision as of 18:58, 19 March 2014

MONOD Round 3

Target identification

  • The specificity of the Round 2 probe set seemed to be very low. Dinh found that 42.5% of the captured targets overlap with repeats. This could explain many off-target reads.
  • In this re-design, I included the RRBS data (ENCODE, GSE52140) for the A549 and HTB56 lung cancer cell line for identifying cancer DMS. In addition, I also added ENCODE RRBS data from normal brain, lung and pancreas as the controls.
  ./find_DMS_PANC_GBM_LC_v3.pl > GBM_PC_LC_DMS_v3.txt
  ../extract_clusters.pl GBM_PC_LC_DMS_v3.txt > GBM_PC_LC_DMS_clusters.v3.txt

Probe design