Short sequence alignment using Minimap2

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3.2 years ago

Sbrillo ▴ 10

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.

assembly minimap2 kmer gRNA pacbio • 1.4k views

ADD COMMENT • link updated 3.1 years ago by GenoMax 141k • written 3.2 years ago by Sbrillo ▴ 10

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Why not use bowtie with -a option to get all locations of where this k-mer matches. That is what you are looking for?

ADD REPLY • link 3.2 years ago by GenoMax 141k

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DO you know if i can get a sam file from bowtie in order to open it on IGV?

ADD REPLY • link 3.1 years ago by Sbrillo ▴ 10

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You sure can. Convert SAM to BAM, sort and index for viewing in IGV.

ADD REPLY • link 3.1 years ago by GenoMax 141k

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