sc13-bioinf
commented
8 years ago EAGER wrongly uses the stats file from the realigned output: (This is after mapping)
output/Sample_JK2760/3-Mapper/JK2760_TTCTGAATGGCGGT_L008_R1_001.fastq.merged.fq.MT_realigned.bam.stats
I have added a CircularMapper pipeline, still need to decide how to use it to avoid calculation of the endgogenous DNA from the realigned stats.
Summary When running EAGER 1.92.9 (1.92.10 in Jena), and using mtCapture mode (+ CircularMapper + mapQ 37) on mtEnriched DNA, the resulting Endogenous DNA (%) column in ReportTable gives the incorrect value. It should give: On Target mtDNA Reads prior DeDup/Reads after C&M
Description and Example Currently, ReportTable takes the % Endogenous DNA from the '*realigned.bam.stats' file in 3-Mapper when mtCapture mode is on. However, this file gives previously the 'input' number of reads into mapping to the whole nu+mt genome, which is a different from the number of reads after C&M prior mapping given in ReportTable, leading to an erroneous % value.
For example Report Table gives: Sample: JK2760 No. reads after C&M: 3,617,343 No mapped reads prior RMDup: 399,317 Mapped Reads after RMDUP: 17907 Endogenous DNA (%): 15.024
The Endogenous DNA of 15% derives from this stats file that gives the following numbers: 2657863 + 0 in total (QC-passed reads + QC-failed reads) [...] 399317 + 0 mapped (15.02% : N/A)
As you can see, the number of 'input reads' into the Mapping in the .stats file is not the same as the one presented after C&M.
The correct endogenous DNA calculation should be (399,317/3,617,343)*100 = 11.03% (on target mt reads / input reads)
Solution When mtCapture mode is turned on, Endogenous DNA from mtCapture mode should be calculated at least as: reads mapping to MTCHR prior DeDup / reads after C&M prior mapping
Or preferably: reads mapping to MTCHR prior map quality filtering and DeDup / reads after C&M prior mapping
Additionally, the number of reads mapping to the whole genome (prior filtering for just mt reads) should be included as a new column.
Example Files EAGER config file EAGER log.log & execution.log Stats log from Clip&Merge and Mapping output folders ReportTable of corresponding run
mtcap_EndoCalc_Issue.zip