Hi this is my first post here, budding bioinformatician.

I have basecalled pod5 files and aligned them at the same time using Dorado while running one of its modification detection models. Using my output BAMs I ran samtools :

samtools view -b -F 0x904 --threads 40 "$input_bam" > "${prefix}_primary.bam"

samtools view -b -q 7 -@ 40 "${prefix}_primary.bam" > "${prefix}_primary_mapq7.bam"

samtools sort --threads 40 -o "${prefix}_primary_mapq7_sorted.bam" "${prefix}_primary_mapq7.bam"

samtools index -@ 40 "${prefix}_primary_mapq7_sorted.bam" 

Can I run nanopolish on the final bam? My aim is to use xpore to do Diferrential RNA modification to analyze change in modification levels b/t wt and KO.

But to run xPore I need to resquiggle with nanopolish and some sources are saying that it only works with guppy which is a precursor of dorado.