No Sequence Segments for secondary alignments in minimap2 while trying to run alignment on ONT data?
Hello all, I was trying to align a set of ONT reads that I have against my reference and I noticed something strange in the generated SAM file. If a read has any secondary alignment, there are no sequence segments present in the output for it. Is this some default behavior for minimap2? I really need the secondary sequence segment for some further analysis. This is the command that I ran.
minimap2 -t 10 -ax map-ont reference.fasta combines_reads.fastq > alignment_out.sam 2> log.txt
I even tried the above command with --secondary=yes command but I still get an empty seq segment for secondary alignments. Could please help me with this?
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