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

From ZhangLabWiki
Jump to navigation Jump to search
mNo edit summary
 
(4 intermediate revisions by the same user not shown)
Line 10: Line 10:
*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]]
*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]]
*ppDesigner output: [[Media:GBM_PC_LC_DMS_probes_v3.txt|GBM_PC_LC_DMS_probes_v3.txt]]
*Removal of probes capturing less than 4 CpG sites
  ../[[Media:filter_probe.txt|filter_probe.pl]] < [[Media:GBM_PC_LC_DMS_probes_v3.txt|GBM_PC_LC_DMS_probes_v3.txt]] > [[Media:GBM_PC_LC_DMS_probes_v3_4cpg.txt|GBM_PC_LC_DMS_probes_v3_4cpg.txt]]
*Dinh helped me to annotate the repeat content of these probes.
*In the final 12k oligo pool, I included all 6466 non-repetitive probes in this set, plus additional 5534 non-repetitive fetal DMR v2 probes in chrs 13/18/21/X to fill up the space.
**ProbeInfo file:[[Media:MONOD_V3_12k_probeInfo.txt|MONOD_V3_12k_probeInfo.txt]]
**Oligo sequenced ordered (V6 primers, N8 UMI):[[Media:MONOD_V3_12k_seq_only.txt|MONOD_V3_12k_seq_only.txt]]

Latest revision as of 19:13, 19 March 2014

MONOD Round 3[edit]

Target identification[edit]

  • 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[edit]

  ../filter_probe.pl < GBM_PC_LC_DMS_probes_v3.txt > GBM_PC_LC_DMS_probes_v3_4cpg.txt
  • Dinh helped me to annotate the repeat content of these probes.
  • In the final 12k oligo pool, I included all 6466 non-repetitive probes in this set, plus additional 5534 non-repetitive fetal DMR v2 probes in chrs 13/18/21/X to fill up the space.