{Plate1}-{Plate2}-{PCRIndex}-{RandomIndex}
, the Plate1 and Plate2 are two plates that multiplexed together by the eight random indexes. The Plate column (see below) is the actual plate that the cell comes from.{Plate}-{MultiplexGroup}-{PCRIndex}-{RandomIndex}
. yap demultiplex
.yap demultiplex
. This equals to CellInputReadPairs
and R2InputReads
.yap demultiplex
.yap demultiplex
. This equals to CellInputReadPairs
and R1InputReads
.yap demultiplex
.yap demultiplex
. This equals to R1InputReads
and R2InputReads
.CellInputReadPairs / sum(CellInputReadPairs of the same multiplex group)
.R1TrimmedReads / R1InputReads
.R2TrimmedReads / R2InputReads
.R1UnuniqueMappedReads / R1TrimmedReads * 100
.R1UnuniqueMappedReads / R1TrimmedReads * 100
.R1DuplicatedReads / R1MAPQFilteredReads
.(1 - R1DeduppedReads(m3c) / R1UniqueMappedReads(m3c)) * 100
.R2MAPQFilteredReads - R2DuplicatedReads
. In mCT mode, reads are further filtered by mC fraction (see FinalDNAReads.)R2DuplicatedReads / R2MAPQFilteredReads
.(1 - R2DeduppedReads(m3c) / R2UniqueMappedReads(m3c)) * 100
.R2MAPQFilteredReads - R2DuplicatedReads
. In mCT mode, reads are further filtered by mC fraction (see FinalDNAReads.)R1FinalBismarkReads + R2FinalBismarkReads
.R1DeduppedReads (m3c) + R2DeduppedReads (m3c)
.mCHmC / mCHCov
mCGmC / mCGCov
mCCCmC / mCCCCov
FinalDNAReads / FinalmCReads
.FinalRNAReads / RNAUniqueMappedReads
CisShortContact + CisLongContact + TransContact
.CisShortContact / TotalContacts
.CisLongContact / TotalContacts
.TransContact / TotalContacts
.