Processing Fiberseq with fibertools
Welcome to the fibertools-rs wiki!
To create useable Fiber-seq data you must first call m6A mods on the PacBio CCS bam using fibertools-rs. First install fibertools-rs with bioconda and then process your bam file using the prediction command.
ft predict-m6a -t 16 input.ccs.bam output.fiberseq.bam This will both make m6A calls and identify nucleosomes on each fiber. This data can then be extracted using ft extract.
Note, the input CCS bam must have average kinetics to be able to call m6A.
Please use pbmm2 for alignment.
To run our automated QC first create the a table with all the fiber-seq data:
ft extract -t 8 <input.bam> --all - | bgzip -@ 8 > sample_name.fiberseq.all.tbl.gz
And then use our QC script to generate a series of QC plots. e.g.
