Why my mapping result is always: mapped (0.00% : N/A)

[JulioRogers]

Hello everyone, I am using minimap2 with a fasta and a fastq files.

The line that I am trying is the following: ./minimap2 -ax map-ont reference.fasta BC10.fastq > output.sam

But the mapping result is always "mapped (0.00% : N/A)". I'm new in this area, and I don't know what could be the problem. Somebody could help me?

[khush876]

Hi,

Did you use nanopre ONT data as a .fastq?

Thanks

[khush876]

./minimap2 -ax map-ont reference.fasta BC10.fastq -o output.sam

[JulioRogers]

Hi,

Did you use nanopre ONT data as a .fastq?

Thanks

Hello, thank you for your reply. Yes, I already used ONT, the problem is the same. I'm thinking that maybe the real problem is the file fastq.

[khush876]

Is reference.fasta file an assembled genome? Do you know how to further use .sam file after mapping the data on ONT?

[wjj666]

Hi, I am using minimap2 (version: 2.20-r1061) with this cmd:

minimap2 -t 100 -k 2g -ax map-hifi -o out.sam ref.fa reads.fa

ref.fa file is a draft assembly, reads.fa file is HIFI reads. The mapping results is always "mapped (0.00% : N/A)", too. Do I need to use HIFI data as a .fastq? But there is nothing wrong when I use the .fasta file with ONT data or PacBio data. Could you please help me with this problem?

These are mapping result when the reads.fa is HIFI data.

11714594 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 0 + 0 mapped (0.00% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)

These are mapping results when the reads.fa is ONT data (-ax map-ont) or PacBio data (-ax map-pb): ONT:

19158851 + 0 in total (QC-passed reads + QC-failed reads) 2834850 + 0 secondary 2734477 + 0 supplementary 0 + 0 duplicates 14992555 + 0 mapped (78.25% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)

PacBio:

42914652 + 0 in total (QC-passed reads + QC-failed reads) 7130745 + 0 secondary 5973951 + 0 supplementary 0 + 0 duplicates 41004572 + 0 mapped (95.55% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)