These are chat archives for cboursnell/transfuse

4th
Feb 2016
Jordi
@jordur
Feb 04 2016 11:46 UTC
Just to notice that in https://github.com/cboursnell/transfuse the parameter "--assembly" in the example command seems to be wrong. Instead it should be "--assemblies", shouldn't?
Chris Boursnell
@cboursnell
Feb 04 2016 13:21 UTC
Yeah it should be assemblies. Cheers for the spot. Will fix now.
How is transfuse working out for you?
Will
@willblev
Feb 04 2016 15:13 UTC
I can't believe it's been over a month since you packaged tranfuse (after my persistent requests)... I have disappeared into a code refactoring black hole- transferring my projects from the last 2 years into iPython notebooks - and am just now getting back to the assembly phase. I will be giving transfuse a go hopefully this month, and will see if merging cufflinks/SOAP/Trinity gives us significantly better assemblies (according to transrate as well as reproducibility between replicates)
Chris Boursnell
@cboursnell
Feb 04 2016 16:46 UTC
I've been doing some tests recently and putting some figures together.
merged.png
This is from several assemblies done with soap varying the size of the kmer used. I aligned the contigs to the genome using blat and then plotted the query coverage on the y against the contigs in order on x
the 'm' line is the five other assemblies merged together with transfuse
the transrate score goes from 0.165 at the highest for the individual to 0.489 for the merged