text: user1135: While going through the HISAT2 manual, one can see this: 
  
  Two alignments for the same individual read are "distinct" if they map
    the same read to different places. Specifically, we say that two
    alignments are distinct if there are no alignment positions where a
    particular read offset is aligned opposite a particular reference
    offset in both alignments with the same orientation. E.g. if the first
    alignment is in the forward orientation and aligns the read character
    at read offset 10 to the reference character at chromosome 3, offset
    3,445,245, and the second alignment is also in the forward orientation
    and also aligns the read character at read offset 10 to the reference
    character at chromosome 3, offset 3,445,245, they are not distinct
    alignments.
  Two alignments for the same pair are distinct if either the mate 1s in
    the two paired-end alignments are distinct or the mate 2s in the two
    alignments are distinct or both.
  Default mode: search for one or more alignments, report each
  
  and then there is -k parameter (analogous to bowtie2 -K parameter)
  which defines: 
  
  HISAT2 searches for up to N distinct, primary alignments for each
    read, where N equals the integer specified with the -k parameter.
    Primary alignments mean alignments whose alignment score is equal or
    higher than any other alignments. It is possible that multiple
    distinct alignments have the same score. That is, if -k 2 is
    specified, HISAT2 will search for at most 2 distinct alignments. The
    alignment score for a paired-end alignment equals the sum of the
    alignment scores of the individual mates. Each reported read or pair
    alignment beyond the first has the SAM 'secondary' bit (which equals
    256) set in its FLAGS field. See the SAM specification for details.
  
  This is a bit confusing, as the first quote means that HISAT2 finds all distinct valid alignment and reports them by default, and the second quote says that when -k option is used, it will only report a subset of alignments which it would have reported by default. Am I correct in this inference or does one needs to use -k option to enable "multi-mapping"?
  
  user96: You said:
  
  ...the first quote means that HISAT2 finds all distinct valid alignment and reports them by default.
  
  Not exactly. The first section you quoted doesn't say it will find and report all distinct alignments, but rather that it would find and report one or more distinct alignments. It's a subtle difference, but an important one.
  That section describes how distinct mappings are defined, not how many are reported. The second section you quoted, as well as the documentation for the -k parameter, are all consistent with this interpretation.
  
  -k <int>        It searches for at most <int> distinct, primary alignments for
                  each read. Primary alignments mean alignments whose alignment
                  score is equal or higher than any other alignments. The search
                  terminates when it can't find more distinct valid alignments, or
                  when it finds <int>, whichever happens first. The alignment
                  score for a paired-end alignment equals the sum of the alignment
                  scores of the individual mates. Each reported read or pair
                  alignment beyond the first has the SAM 'secondary' bit (which
                  equals 256) set in its FLAGS field. For reads that have more
                  than <int> distinct, valid alignments, hisat2 does not guarantee
                  that the <int> alignments reported are the best possible in
                  terms of alignment score. Default: 5 (HFM) or 10 (HGFM)
  
                  Note: HISAT2 is not designed with large values for -k in mind,
                  and when aligning reads to long, repetitive genomes large -k can
                  be very, very slow.
  
  
  By default, 5 or 10 distinct mappings are reported (depending on the mode), but you can control this with the -k parameter.
  
original_text: 1135: <p>While going through the <a href="https://ccb.jhu.edu/software/hisat2/manual.shtml" rel="nofollow noreferrer">HISAT2 manual</a>, one can see this: </p>
  
  <blockquote>
    <p>Two alignments for the same individual read are "distinct" if they map
    the same read to different places. Specifically, we say that two
    alignments are distinct if there are no alignment positions where a
    particular read offset is aligned opposite a particular reference
    offset in both alignments with the same orientation. E.g. if the first
    alignment is in the forward orientation and aligns the read character
    at read offset 10 to the reference character at chromosome 3, offset
    3,445,245, and the second alignment is also in the forward orientation
    and also aligns the read character at read offset 10 to the reference
    character at chromosome 3, offset 3,445,245, they are not distinct
    alignments.</p>
    
    <p>Two alignments for the same pair are distinct if either the mate 1s in
    the two paired-end alignments are distinct or the mate 2s in the two
    alignments are distinct or both.</p>
    
    <p>Default mode: search for one or more alignments, report each</p>
  </blockquote>
  
  <p>and then there is -k parameter (analogous to bowtie2 -K parameter)</p>
  
  <p>which defines: </p>
  
  <blockquote>
    <p>HISAT2 searches for up to N distinct, primary alignments for each
    read, where N equals the integer specified with the -k parameter.
    Primary alignments mean alignments whose alignment score is equal or
    higher than any other alignments. It is possible that multiple
    distinct alignments have the same score. That is, if -k 2 is
    specified, HISAT2 will search for at most 2 distinct alignments. The
    alignment score for a paired-end alignment equals the sum of the
    alignment scores of the individual mates. Each reported read or pair
    alignment beyond the first has the SAM 'secondary' bit (which equals
    256) set in its FLAGS field. See the SAM specification for details.</p>
  </blockquote>
  
  <p>This is a bit confusing, as the first quote means that HISAT2 finds all distinct valid alignment and reports them by default, and the second quote says that when -k option is used, it will only report a subset of alignments which it would have reported by default. Am I correct in this inference or does one needs to use -k option to enable "multi-mapping"?</p>
   96: <p>You said:</p>
  
  <blockquote>
    <p>...the first quote means that HISAT2 finds all distinct valid alignment and reports them by default.</p>
  </blockquote>
  
  <p>Not exactly. The first section you quoted doesn't say it will find and report <em>all</em> distinct alignments, but rather that it would find and report one or more distinct alignments. It's a subtle difference, but an important one.</p>
  
  <p>That section describes how distinct mappings are defined, not how many are reported. The second section you quoted, as well as the documentation for the <code>-k</code> parameter, are all consistent with this interpretation.</p>
  
  <blockquote>
  <pre><code>-k &lt;int&gt;        It searches for at most &lt;int&gt; distinct, primary alignments for
                  each read. Primary alignments mean alignments whose alignment
                  score is equal or higher than any other alignments. The search
                  terminates when it can't find more distinct valid alignments, or
                  when it finds &lt;int&gt;, whichever happens first. The alignment
                  score for a paired-end alignment equals the sum of the alignment
                  scores of the individual mates. Each reported read or pair
                  alignment beyond the first has the SAM 'secondary' bit (which
                  equals 256) set in its FLAGS field. For reads that have more
                  than &lt;int&gt; distinct, valid alignments, hisat2 does not guarantee
                  that the &lt;int&gt; alignments reported are the best possible in
                  terms of alignment score. Default: 5 (HFM) or 10 (HGFM)
  
                  Note: HISAT2 is not designed with large values for -k in mind,
                  and when aligning reads to long, repetitive genomes large -k can
                  be very, very slow.
  </code></pre>
  </blockquote>
  
  <p>By default, 5 or 10 distinct mappings are reported (depending on the mode), but you can control this with the <code>-k</code> parameter.</p>
  