nanoporetech
pileup-hemi
I want run hemi-methylation in 5mC context... modkit pileup-hemi -o ftr.bed --motif C 0 -r mtDNA.fasta -t 32 --no-filtering ftr.bam... i am getting error as Error! motif must be palindromic for pileup-hemi. please help
Hello @partha434,
The pileup-hemi command is meant for duplex Nanopore data where you have base modification calls on the (+)-strand and the (-)-strand combined into a single duplex read. Then is aggregates the patterns of double-stranded calls. For example, if you use --motif CG 0 it will count the occurrences of 5mC/5mC, C/5mC, 5mC/C, C/C. More documentation can be found here. If you have duplex reads and want to perform a normal pileup, modkit pileup will handle duplex calls as well.
