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
- I pretty much followed the same design as the MONOD Round 2 probes.
- Input files: GBM_PC_LC_DMS_clusters_v3_input_plus.txt;GBM_PC_LC_DMS_clusters_v3_input_minus.txt
- Job files:jobFile_GBM_PC_LC_DMR_150_plus.pl;jobFile_GBM_PC_LC_DMR_150_minus.pl
- ppDesigner output: GBM_PC_LC_DMS_probes_v3.txt