Detection of modifications
In order to detect and annotated modified positions, modPhred scans read alignments and for every position of reference genome/transcriptome it calculates
depth of coverage,
basecall accuracy,
modification frequency
and median modification probability.
Those values are reported into mod.gz
file.
By default, modPhred reports only sites with modifications fulfilling following criteria:
minimum mapping quality of 15 - only reads with mapping quality of 15 or more are considered
minimum sequencing depth of 25 - at least 25 reads for given positions
at least 0.05 frequency of modification - at least 5% of reads being modified for this position
at least 0.5 modification probability - only bases with modification probability of 50% or more are considered as truly modified.
The default values can be adjusted with several parameters:
./run -h
...
-m --mapq min mapping quality [15]
-d --minDepth min depth of coverage [25]
--minModFreq min modification frequency per position [0.05]
--minModProb min modification probability per base [0.5]
...