Hello, I am curious about how cufflinks chooses 5' ends for de novo annotations (i.e. one that uses only bam file information) and wonder if the models can be improved with some parameters:
I am using cufflinks v2.0.2 and running the following command:
cufflinks --min-frags-per-transfrag 1000 -j 0.3 --library-type ff-firststrand -o testOut testregion.bam
As you can see from the attached image, cufflinks generates a model with a 5' UTR that extends far beyond the annotated gene and density of the reads from the paired-end data. Is there any way to more greatly constrain cufflinks so it would trim the 5' end to an appropriate position?
Any help would be greatly helpful, thanks!
I am using cufflinks v2.0.2 and running the following command:
cufflinks --min-frags-per-transfrag 1000 -j 0.3 --library-type ff-firststrand -o testOut testregion.bam
As you can see from the attached image, cufflinks generates a model with a 5' UTR that extends far beyond the annotated gene and density of the reads from the paired-end data. Is there any way to more greatly constrain cufflinks so it would trim the 5' end to an appropriate position?
Any help would be greatly helpful, thanks!