Which strand to use in RNA modification?

[guangzhaocs]

Hi,

I use the tombo detect_modifications alternative_model to dectect the RNA m5C modification. Then I use the tombo text_output browser_files to get the resluts.

I get fraction_modified_reads.minus.wig and fraction_modified_reads.plus.wig two files. I think one file is for fwd_strand while another is for rev_strand.

Because my data is RNA and my reference sequence is synthetic sequence or transcriptome. So in this case, which one should I use in fraction_modified_reads.minus.wig and fraction_modified_reads.plus.wig ?

I think the raw file in fast5 is form 3' to 5' (RNA is currently sequenced in the 3’ to 5’ direction). So in RNA sequencing, why here have two files for plus strand and minus strand?

Thanks!