I used Salmon to quantify RNA at the transcript level. Is there a way to map this data into a format that can be viewed in IGV?
A related question, i also tried another method of quantifying where i aligned the read with STAR and counted with GenomicAlignments. The counts from this method is easily double that of the count from Salmon. With some transcripts counted almost 8x to 10x more. I did a Pearson's correlation and it return as value of 0.95, so i'm guessing it would not significantly affect me if i am doing genome wide analysis. But i am still curious as to how this discrepancy came about.
Any input will be greatly appreciated