piquant
piquant copied to clipboard
lweasel
A pipeline to assess the quantification of transcripts.
Some quantifiers (e.g. Cufflinks) can produce vastly inflated FPKM values for very short transcripts, in which case it is recommended to simply ignore the values produced for such isoforms. Unfortunately...
Simple fix to string split in gtf.py, can't believe I didn't run across this before.
The Flux simulator seems to not respect the _effective length_ of transcripts during it's simulation. This means that quantification tools that "correctly" adjust for effective length will be penalized for...
It would be helpful to clarify the output that is expected to be seen at each stage. For example, when running "create_reads", all that will immediately be seen is messages...
When simulating reads, the location of a GTF file containing noise transcript definitions should need only to be specified if background noise is being simulated (i.e. for values of "--noise-perc"...