Peng Ni

use newer tensorflow, not only 1.8.0

add options and code (_ref_reader.py_ and related) for RNA data

may be it is better to add a "--region" option in the _extract_features_ and _call_methy_ modules, to only extract and testing the basemods in the interested regions.

recommended threshold for the log likelihood ratio

4

Hi @hasindu2008 and all, For the `f5c meth-freq` step, is the reommended threshold for the log likelihood ratio still 2.5, or should be 2.0 as nanopolish has changed? Thank you...

pod5/slow5 support

1

pod5: https://github.com/nanoporetech/pod5-file-format slow5: https://github.com/hasindu2008/slow5lib use tombo api to resquiggle (#5).

modbam format support

1

support modbam output for viewing modifications in genome browsers

tabix/pytabix/gzip support to lower memory/speed up call_freq step

2

Maybe try redesign call_freq module, use bed-gzip-tabix-bed.gz/tbi.

tombo annotate fast5 with fastq, fails without sequence_summary file. what is the reason? dependencies too new?

test pipeline for haplotype dna methylation calling, add necessary scripts

add docker container

1

Write dockerfile, add docker/singularity container and test it. helping solving vba compression issue and other issues?