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
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
minimap2 -ax splice -ub -k14 ref.fa direct-rna.fq > aln.sam
It did not work better.
FYI: I am trying to find answer for this from few days. I have posted this question on Biostars before. I did not get any response. Hence, I am trying to find the answer here.
Thank you in advance. I really appreciate any help.