<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>

<rna-seq><phylogenetics><salmon>
Get Salmon mapping/alignment summary
# Get Salmon mapping/alignment summary

(Asked by: username_0 on 2021-05-12)

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?

**Tags:** rna-seq, phylogenetics, salmon

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## 0 answers

