Hi everyone.
We have a trinity assembly that presumably contains lots of isoforms/hybrids/paralogs etc.
We have a second organism in there at a low level so don't want to filter out isoforms with low read evidence as others may.
I'm aware trinity creates a component that it splits to isoforms but this component file doesn't appear to be generated as a fasta at any time.
How can we filter out the best transcript models before we do some in depth annotation? Can we run cuffmerge on a trinity assembly eg put two copies of the assembly in as two transcriptomes and get it to combine with itself?
Any other ideas?
Cheers,
FGPonce
We have a trinity assembly that presumably contains lots of isoforms/hybrids/paralogs etc.
We have a second organism in there at a low level so don't want to filter out isoforms with low read evidence as others may.
I'm aware trinity creates a component that it splits to isoforms but this component file doesn't appear to be generated as a fasta at any time.
How can we filter out the best transcript models before we do some in depth annotation? Can we run cuffmerge on a trinity assembly eg put two copies of the assembly in as two transcriptomes and get it to combine with itself?
Any other ideas?
Cheers,
FGPonce
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