Question: aligner for 1D^2 oxford nanopore data
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gravatar for KVC_bioinfo
2.7 years ago by
KVC_bioinfo510
Boston
KVC_bioinfo510 wrote:

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

nanopore 1d^2 minimap2 • 1.0k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by KVC_bioinfo510
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