Short sequence alignment using Minimap2
Hello,
I'm trying to align a short sequence ( 25 bp kmer) to a subset of pacbio reads using minimap2 in order to map the kmer and have an idea of his distribution along with the pacbio reads (i'm 100% sure that the pacbio reads contain the kmer sequence since I selected those pacbio after a bowtie alignment using -v 0)
Every time I run the command the sam output file doesn't contain any information regarding the matches.
This is the command that i used :
minimap2 -a -o pacbio-vs-kmer12.sam -t 8 pacbio-kmer_78734079-unique.fasta kmer-78734079-12.fasta
I need the sam file in order to visualize the kmer position on IGV.
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Why not use
bowtiewith-aoption to get all locations of where this k-mer matches. That is what you are looking for?DO you know if i can get a sam file from bowtie in order to open it on IGV?
You sure can. Convert SAM to BAM, sort and index for viewing in IGV.