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Oshlack / Corset

Software for clustering de novo assembled transcripts and counting overlapping reads
https://github.com/Oshlack/Corset/wiki
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Read counts not being filtered #20

Open MarcosDomingues97 opened 2 years ago

MarcosDomingues97 commented 2 years ago

Hi, I ran corset in a single sample with the default parameters and got clusters with read counts below 10, some of which with zero counts inclusively. Is this to be expected?

Thanks in advance.

nadiadavidson commented 2 years ago

Hi, Yes, this comes about because reads which are shared between more than one cluster get randomly assigned to a cluster. Meaning that a cluster may have originally had 10 or more reads mapping, but some of these are reassigned to avoid double counting.

There are a few related threads on this in https://groups.google.com/g/corset-project?pli=1 and closed issues which you might like to look at also. Cheers, Nadia.