dRNAmain

dRNAmain moudle includes fast5-basecall, mapping and transcriptome count.

Concept

build of reference file

The ref in config.yml need to be build in manual, requiring fastq file and annotation file(in gtf/gff3) Since the following dRNAas needs gtf file, we advise you to choose gtf annotation file and use gffread to convert to gff3.

gffread genome.gtf -o- > genome.gff3

Then generate fastq file for transcriptome mapping.

gffread -F -w transcriptome.fa -g genome.fa genome.gff3 

selection of f5c version

For f5c, it offers two version called f5c_x86_64_linux and f5c_x86_64_linux_cuda. cuda version is for GPU, so if you only run with CPU, please change dRNAmain.py line 159

f5c_x86_64_linux_cuda index --slow5 {input[1]} {input[0]}

to

f5c_x86_64_linux index --slow5 {input[1]} {input[0]}

Choice of cfg files

The cfg files are located in /ont-guppy/data/ You can assign the specific file based on the chips’ version your experinment choose.