Open lancer-lu opened 4 years ago
I had a similar issue and ended up splitting the BAM files into those that only contain paired-end reads and those that contain single-end reads. Then you can supply the former with --frags
and the latter with --unpaired
. This is very unpractical for large BAM files, though, therefore, currently I run the mapper twice for paired and unpaired reads.
**Hi, I'm confused about the option: --bam/--jumps/--frags/unpaired. When my bam file contains single-end and paired-end reads, which option should I choose?
In the beginning, my reads is paired. I merged the paired-end reads to better identify the species when analyzing metagenome data, but part of the reads can't merge , so the bam file contains single-end and paired-end reads.