--ref <REFERENCE_FASTA> is to select the reference genome or transcriptome

[Tang-pro]

@rmp

When I want to perform m6A analysis and use modkit pileup to identify methylation information, should I specify the reference genome or the reference transcriptome with the --ref <REFERENCE_FASTA> option?

[ArtRand]

Hello @Tang-pro,

You should use the FASTA that you aligned the reads to. However, this argument is only required if you're using the --motif options.

[Tang-pro]

Hi @ArtRand

the BAM file generated from aligning sequencing reads to a transcriptome
I have a doubt regarding the following commands:
Without using --ref:
modkit pileup Y2_5_2.bam Y2_5_2.bed --log-filepath Y2_5_2.log -t 20 --with-header
What kind of positions are obtained here?
With --ref:
modkit pileup ../Y2_5_2.bam Y2_5_2.bed --ref transcripts.fa --log-filepath Y2_5_2.log -t 20 --with-header --motif DRACH 2
Are the positions obtained here relative to the starting position of the transcript?
So adding --refe or not, what is the difference in position?