Hello, I am new here, seeking some advice on a problem I am faced in a current project of mine.
I am trying to simulate reads from an assembled sample genome in order to align to my reference variation graph in order to determine reads that map correctly and do not.
I have generated a polished assembly of the sample using my reference and the bam files from the sample. I am currently using minimap2 to align my sample fasta to my reference genome to determine where my sample aligns to the reference, so that when I simulate reads and align them to my variation graph I can determine if a read mapped correctly or not.
I am having trouble with the output paf from minimap2. I can determine the positions on the reference that a contig has mapped to, but I am not able to identify indels in those alignments. Hopefully my problem makes sense, I can try to clarify further.
If you have any advice or experience doing something similar, I would greatly appreciate it.
I am trying to simulate reads from an assembled sample genome in order to align to my reference variation graph in order to determine reads that map correctly and do not.
I have generated a polished assembly of the sample using my reference and the bam files from the sample. I am currently using minimap2 to align my sample fasta to my reference genome to determine where my sample aligns to the reference, so that when I simulate reads and align them to my variation graph I can determine if a read mapped correctly or not.
I am having trouble with the output paf from minimap2. I can determine the positions on the reference that a contig has mapped to, but I am not able to identify indels in those alignments. Hopefully my problem makes sense, I can try to clarify further.
If you have any advice or experience doing something similar, I would greatly appreciate it.