Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine P C R D u p l i c a t e R e m o v a l  Work Log 05/10 

Quality and alignment status after PCR duplicate removal (No 35) Original 34677439 + 0 in total (QC-passed reads + QC- failed reads) 0 + 0 duplicates 29995490 + 0 properly paired (86.50%:nan%) 32605024 + 0 with itself and mate mapped 2072415 + 0 singletons (5.98%:nan%) 276858 + 0 with mate mapped to a different chr 165466 + 0 with mate mapped to a different chr (mapQ>=5) After PCR duplicate removal 23301708 + 0 in total (QC-passed reads + QC- failed reads) 0 + 0 duplicates 19065893 + 0 properly paired (81.82%:nan%) 21229293 + 0 with itself and mate mapped 2072415 + 0 singletons (8.89%:nan%) 276858 + 0 with mate mapped to a different chr 165466 + 0 with mate mapped to a different chr (mapQ>=5) Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 2 32.7% duplicates Command to view alignment status samtools) $ samtools flagstat Two tools can remove PCR duplicates: samtools) $ samtools rmdup Picard) $ java –jar MarkDuplicates.jar INPUT= OUPUT= … 

Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 3 

Significant genes No42 vs No35 •  before PCR duplicate removal •  20(21) unique annotated of 86 genes •  NM_205489, NM_213575, NM_001037271, NM_001097538, NM_001004376, NM_001031016, NM_001030893, NM_001031138 •  after PCR duplicate removal •  13 unique annotated of 62 genes •  NM_213577 •  12 both showed: •  NM_001005346, NM_001005808, NM_204493, NM_001044636, NM_001005571, NM_001194927, NM_001001753, NM_205471, NM_001252016, NM_001113167, NM_204674, NM_204114 Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 4