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====Capture efficiency & bias==== *Check the capture efficiencies for all probes using [[Media:bam2probeEfficiency.txt|bam2probeEfficiency.pl]]: Batch processing script: [[Media:get_probeEfficiency_all_files.txt|get_probeEfficiency_all_files.sh]]; Merge all files into a matrix: ./[[Media:get_probeEfficiency_matrix.txt|get_probeEfficiency_matrix.pl]] > [[Media:131227_MiSeq_V4_probeEfficiency_matrix_UMI_20Mar14.txt|131227_MiSeq_V4_probeEfficiency_matrix_UMI_20Mar14.txt]] Some probes seemed to have very different capture efficiencies between cancer and whole blood. This could be due to the fact that two probes were synthesized for H1/H2 that having CpG sites and that the "C" probes have higher annealing efficiencies. I plotted the T-stat (between cancer and whole blood) against the number of CpG sites within the capture arms H1/H2, or within the insert. There was a positive correlation between the number of CGs in H1/H2, but that only explain ~10% of the variability. There seems to be another major factor unknown. [[Image:MONOD_V1_Capture_bias_vs_CG_H1H2.png|400px]][[Image:MONOD_V1_Capture_bias_vs_CG_insert.png|400px]] *I decided to focus on the analysis on a subset of "stable probes" that have similar efficiency between cancer and whole blood.
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