With HISAT2, after the alignment of fastq files you get an alignment summary like this:

20000 reads; of these:
  20000 (100.00%) were unpaired; of these:
    1247 (6.24%) aligned 0 times
    18739 (93.69%) aligned exactly 1 time
    14 (0.07%) aligned >1 times
93.77% overall alignment rate

Is it possible to get this information with Salmon?


1 Answer 1


The salmon output log contains a line with [info] Mapping rate which allows to calculate how many reads went mapped or unmapped. Is that sufficient? It should be in the logs folder of the directory salmon creates per sample.


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