Hello, I have a paired end reads and I am running bbmerge to merge the reads into a fastq file. However, in log file, I see high percentage of no solution reads.
Pairs: 681070 Joined: 262235 38.503% Ambiguous: 15798 2.320% No Solution: 403037 59.177% Too Short: 0 0.000% Adapters Expected: 798584 58.627% Adapters Found: 6 0.000% Avg Insert: 213.9 Standard Deviation: 20.3 Mode: 222 Insert range: 35 - 294 90th percentile: 222 75th percentile: 222 50th percentile: 222 25th percentile: 221
I have two questions and appreciate any help:
- Any idea what might be the cause of this high percentage of no solution reads?
- What my options are to find the reason for this?
To find the root cause the only thing I can think of is to map the unpaired reads (those did not merge) to the reference and look at the alignment or try to manually pair them.