Thank you very much for developing this wonderful tool. I am trying to run methalign at the moment but was confused with the codes indicated in the tutorial page. Initially, the instruction was to align the PoreC reads to the contig assembly using the code:
bammap2 -t 40 -x lr:hq --secondary=yes contigs.fasta porec_reads.bam > porec.align.bam
After this, we run the methalign with:
methalign -t 20 contigs.fasta output.methyl.bg porec.reads*.bam -o porec.align.refined.paf.gz
I just wanted to clarify if the 'porec.reads*.bam' file in the methalign code refers to the output of the first code, thus the ' porec.align.bam', above? Your response will be much appreciated. Thanks!
Thank you very much for developing this wonderful tool. I am trying to run methalign at the moment but was confused with the codes indicated in the tutorial page. Initially, the instruction was to align the PoreC reads to the contig assembly using the code:
bammap2 -t 40 -x lr:hq --secondary=yes contigs.fasta porec_reads.bam > porec.align.bam
After this, we run the methalign with:
methalign -t 20 contigs.fasta output.methyl.bg porec.reads*.bam -o porec.align.refined.paf.gz
I just wanted to clarify if the 'porec.reads*.bam' file in the methalign code refers to the output of the first code, thus the ' porec.align.bam', above? Your response will be much appreciated. Thanks!