Question regarding aligning two fastq files

[Le1223]

Hello,

I am currently using minimap2 v2.26 and I have a question regarding aligning two fastq files. I have used the following commands:

minimap2 -cx map-ont A.fastq B.fastq --secondary=no > mapA.paf
minimap2 -cx map-ont B.fastq A.fastq --secondary=no > mapB.paf

However, I have noticed that the resulting mapA.paf and mapB.paf files show a significant difference.I would like to understand the reason behind this discrepancy.
Could you please provide any insights or suggestions on how I can assess the sequence information of these two fastq files?

Thank you for your assistance.

Best regards.

[Le1223]

In the example above, the sequence “496a10c7-0dd2-4d88-83c1-7bf6a00cc8ab” has completely different results in the two paf files. Why is that?

[lh3]

This is expected. Other sequences in the reference file will affect alignment.