I have 2 libraries one of them is an illumina mate-pair library. I ran Ray forcing insert size and got a not-so-bad assembly, but the scaffold result wasn't so different from the contig result which was surprising. I wanted to be sure of my distances so I let it guess them. I was expecting 2 peaks for the mate library, but got none.
I ploted the attached distribution (attached), and it does identify a pair peak, but the broad mate distances are not picked up. Not the best library, but there clearly is something there. Is there a way to tell Ray manually that there are 2 distributions in a library? If not, should I only give the mate distribution 4.7k +- 1k or not use the Ray scaffolder and use something else? Thanks
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