Hey there, I've been trying to use alevin-fry on a few single-cell datasets for isoform discovery. So far I've been able to run the quant command successfully and was able to return the 5 file output from this command, but this concerns the gene quantification (using cr-like). I know one of the input files for this is a t2g reference matrix, so I was wondering if there was any way to be able to get transcripts from the final step instead of just the gene they're all mapped to.
I was able to find a few past cases of people using alevin-fry with a t2t map input instead of a t2g map input, but haven't been able to get the same commands to run successfully after making a t2t map, and looking through the resolution strategy options for the quant command I wasn't sure if any of these would be a better option for this.
Any guidance would be greatly appreciated, thanks!
Hey there, I've been trying to use alevin-fry on a few single-cell datasets for isoform discovery. So far I've been able to run the quant command successfully and was able to return the 5 file output from this command, but this concerns the gene quantification (using cr-like). I know one of the input files for this is a t2g reference matrix, so I was wondering if there was any way to be able to get transcripts from the final step instead of just the gene they're all mapped to.
I was able to find a few past cases of people using alevin-fry with a t2t map input instead of a t2g map input, but haven't been able to get the same commands to run successfully after making a t2t map, and looking through the resolution strategy options for the quant command I wasn't sure if any of these would be a better option for this.
Any guidance would be greatly appreciated, thanks!