hello,

I am wondering if anyone has tried aligning 1d^2 RNA-seq data. I am trying that on minimap2. It is giving me very low ~50% of mapped reads. it gives ~95% mapped reads for 1D.

I am using the following command for 1d and 1d^2:

minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam

Update:

I also tried to play around the command using :

minimap2 -ax splice -k14 -a ref.fa direct-rna.fq > aln.sam
minimap2 -ax splice -ur -k14 ref.fa direct-rna.fq > aln.sam

It did not work better. TIA