text: user10386: 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?
  
  user-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.
  
original_text: 10386: <p>With HISAT2, after the alignment of fastq files you get an alignment summary like this:</p>
  <pre><code>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 &gt;1 times
  93.77% overall alignment rate
  </code></pre>
  <p>Is it possible to get this information with Salmon?</p>
   -1: <p>The <code>salmon</code> output log contains a line with <code>[info] Mapping rate</code> which allows to calculate how many reads went mapped or unmapped. Is that sufficient? It should be in the <code>logs</code> folder of the directory <code>salmon</code> creates per sample.</p>
  