The mix option takes as input short-read data and long-read data. However, in my case, I have both PacBio and Nanopore data. The mix option does not allow 3 inputs.
So here is how I am running it. Please let me know if I should do this differently.
If PacBio and Nanopore data belong to the same sample, I am combining them using samtools merge. I still have 40 samples for long read and 40 for short read.
Next, I am assembling them using reference genome as guide. Here I use the --mix option. This generates a GTF file for each sample.
Next, I am merging the data using stringtie merge, and including the reference annotation with the -G option. What I notice is that alternative first isoforms quite often get collapsed and removed, which is why it made sense to include the reference genome.
Following this, I am using this annotation to then compute expression, using the -e option, and again the --mix option.
After this you can run prepDE, etc for downstream analysis.
The mix option takes as input short-read data and long-read data. However, in my case, I have both PacBio and Nanopore data. The mix option does not allow 3 inputs. So here is how I am running it. Please let me know if I should do this differently.
After this you can run prepDE, etc for downstream analysis.