Do you imagine I could/should use different parameters when my bam file was produced by Longranger, the aligner for 10x Genomics reads?
The major difference is that reads are aligned in linked groups, which align only together to the same contig/scaffold. I believe then that alignment is of better quality, but perhaps lower coverage. Does it make sense to ask Pilon to be even more sensitive to the mapped reads in contrast with a PacBio reference?
Hi,
Do you imagine I could/should use different parameters when my bam file was produced by Longranger, the aligner for 10x Genomics reads?
The major difference is that reads are aligned in linked groups, which align only together to the same contig/scaffold. I believe then that alignment is of better quality, but perhaps lower coverage. Does it make sense to ask Pilon to be even more sensitive to the mapped reads in contrast with a PacBio reference?
Cheers, Ricardo