minimap2: aligning ambigious sequence containing N to fastq reads.

Question

[vinaykusuma]

I have a fasta file called barcode masked.fa

Ex:

>Orf1_ab  
AGAGCAGCAGAAGTGGCACNNNNNNNNAGGTGATTGTGAAGAAGAAGAG

Trying to align this on my nanopore reads with minimap.
I am not able to figure out option to do that.
I expect my reads in fastq to not match at those 10bp (denoted by N) in fasta
but should align to the upstream and downstream sequence of N in fastq.

my command is

minimap2  -t 4 -ax map-ont  barcode_masked.fa  all_pass_files.fastq > P5_masked_aln_reads.sam

Currently i get no alignments in my .sam file.
Any help will be appreciated. Thank you.

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[GenoMax]

Is that a real read? You could try a small k-mer size.

minimap2 paper says the following:

works with accurate short reads of ≥100 bp in length

[vinaykusuma]

Thanks for that, But i tried with 51 bp and i got lot of hits in my sam file. Then i compared the count of hits with 51M in cigar to my grep count searching for exact match of 51bp seq and i am getting more matches with minimap. so, technically minimap is working. I looked at some alignments manually too, looked fine to me. But I will surely look again, Thanks for that.

[WouterDeCoster]

But why? What is the aim of this?

[GenoMax]

See: C: minimap2: aligning multiple regions to a read in a fastq

[vinaykusuma]

I want to get count of sequences(accounting subsitution errors) in fasta file. I have lot of data so i think the fastest way is to use a aligner. I tried writing a script, using bbduk.sh but the become slow with lots of data.

[GenoMax]

I tried writing a script, using bbduk.sh but the become slow with lots of data.

I find it hard to believe that bbtools programs are slow. Most are all multi-threaded (including bbduk) and will run rings around any program (short of something written in native c++). If you can tell me what you were trying to do (with exact bbduk command) we can see if that can be optimized.