Can we use refined and unrefined bins from a sample together?

[Jigyasa3]

Dear @dparks1134 @kata198

I successfully ran refineM on my samples and obtained filtered bins. But if the starting number of bins in my sample is 20, refineM produces only 1-2 filtered/refined bins.

I wanted to ask if it is feasible to use the unrefined/original bins and refined ones together for a sample? Secondly, If refineM doesn't refine all the bins in a sample, does that mean that those bins cannot be refined by the algorithm?

Looking forward to your reply!

[donovan-h-parks]

Hi. RefineM treats each bin independently. There should be no concerns in using both the refined and unrefined bins as your final set of MAGs. RefineM uses conservative default values to ensure it doesn't erroneously remove contigs that should be in the bin. You could explore these values. Otherwise, the results indicate that the majority of your bins could not be improved using the methods implemented in RefineM. You could also consider MAGpurify which is another tool for refining bins: https://github.com/snayfach/MAGpurify

[Jigyasa3]

Dear @dparks1134

Thank you so much for replying and for the suggestion to use MAGpurify!