Short sequence alignment using Minimap2
0
0
Entering edit mode
7 months ago
Sbrillo • 0

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 • 523 views
ADD COMMENT
1
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1619 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6