Open mkellom opened 2 years ago
Also, do you know if using the actual contigs for creating a sorted alignment yields much better results than using pseudo contigs from concatenated bins? Or are bins merged just as well either way?
Sorry I was away for a while. I dont have a benchmark dataset that I can share at the moment. You can force it by simply splitting a single eukaryotic MAG into two bins. But of course this would be an artificially created dataset.
I hope I can share datasets soon (Send me an email and I can share some accessions).
I am also working on a test case for the tutorial, but want to keep it simple, and thats hard to create.
Regarding the alignments: In our pipeline we use concatenated bins but I dont see any issues using the assembly or the concatenated bins. Usually they are very similar.
If contigs are in multiple bins this whole process needs to be re-evaluated though, as currently the scripts assume a contig is in a single bin.
I am not sure if that answers the question?
Yes, it does. Thank you!
Do you have a set of sample bins where you know merging should occur?
I have been running the bwa bin merging steps on some bin folders and so far no merging has occurred. So I'm curious if you have a working positive control sample set that you recommend.
Thank you