Found frac=0.000 in output of ipdSummary.py

[noirot]

Same problem as the issue #8 I ran /save/smrtanalysis/current/analysis/bin/ipdSummary.py --verbose --methylFraction --identifyMinCov 10 --minCoverage 10 --outfile epigenet --mapQvThreshold 30 --numWorkers 10 --identify m6A,m4 C --reference genome.fasta merged.cmp.h5

I get on all my analysis ( 10 ) few lines with a frac=0. I can provide one input file. I join a extraction of the output gff file (one file with the 5000 first lines, and one with all the lines with frac=0.000). Here some numbers of the whole output file : NB_position_gff : 980352

_M4C : 839119

average(frac) : 0,7706 m4C_frac==0 : 8124 m4C_frac==1 : 215466

M6A : 141233

average(frac) : 0,7333 m6A_frac==0 : 51 m6A_frac==1 : 9740

example.zip

How does it possible to have methylation with a fraction at 0 ? Cheers, Céline

[mdrishti]

I am getting the same error. I am not sure how to resolve this issue. If you have any hint, please let me know