Output does not include 3' ends of reads

[esh97]

Hello,

Thanks for creating this tool! I've used it previously with RNA002 sequences, and the m6A output data used to reach the 3' end of my reads, however, with the RNA004 data, it now stops about 500 nucleotides from the 3' end of my reads. This is where the majority of the coverage is, so I'm not sure why this region is not included in the output.

Thanks for your help!
Ethan

[esh97]

Hello,

I'm following up on this issue. I have rerun my RNA002 data with version 1 and version 2 of m6anet, and only version 2 is truncating my reads at the 3' end. Is this an issue that can be easily fixed?

Thanks!
Ethan

[yuukiiwa]

Hi Ethan (tagging you here @esh97),

Can you provide the commands for each of the m6anet versions you run, please?

Thanks!

Best wishes,
Yuk Kei

[esh97]

For both version 1 and 2, I run this nanopolish command to generate an eventalign:

nanopolish eventalign --reads merged.fastq --bam sorted.bam --genome ref.fasta --scale-events --signal-index --threads=50 > eventalign.txt

For version 1, I run the following m6anet commands:

m6anet-dataprep --eventalign eventalign.txt --out_dir m6anet/ --n_processes 4
m6anet-run_inference --input_dir m6anet/ --out_dir m6anet/m6a_mods/ --infer_mod_rate --n_processes 4

For version 2, I run the following commands:

m6anet dataprep --eventalign eventalign.txt --out_dir m6anet/ --n_processes 4
m6anet inference --input_dir m6anet/ --out_dir m6anet/m6anet2/

Thanks for your help!
Ethan