I have found Salmon a very good tool to run a set of RNA-seq reads against a fasta file and get meaningful results. However, I would like to get unique hits. Is the default output unique or not? If not, is there a way to change the settings to get unuiqe reads?
Salmon counts each read once (uniquely) per transcript summary. However, the same read may contribute to the count for more than one transcript summary.
Details here: http://salmon.readthedocs.io/en/latest/file_formats.html
Thanks! Jen, Galaxy team