text: user1075: I have this read in my BAM file. It maps on chromosome 1.
  I open this BAM file in IGV, and I can see the alignment on chromosome 1.
  But when I open this file in R with Rsamtools:
  bamContigsCel <- Rsamtools::scanBam('output/alignment/pacbio/bwa/ref     /bristolAssemblySorted.bam', param = Rsamtools::ScanBamParam(what = Rsamtools::scanBamWhat(), flag = Rsamtools::scanBamFlag(isMinusStrand = FALSE), tag = bamTags))[[1]]
  
  I then check if the read maps to chromosome 1 in my R object but I cannot find it.
  bamContigsCel$rname[bamContigsCel$qname == '000000F|arrow']
  [1] II II IV
  Levels: I II III IV MtDNA V X
  
  But if I look at the BAM file, it's there. Why isn't Rsamtools importing my read into R?
  $ samtools view bristolAssemblySorted.bam | grep -n '000000F' | head  -c80
  000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   0 0   GAAGCTGTCTAAACTTTGGC
  
  Cross-posted on biostars
  
  user77: Note the flag; that read is mapped in a reverse-complemented manner, so isMinusStrand = FALSE is filtering it out. I tested this by making a BAM file with only that read:
  @SQ SN:I    LN:1000000
  000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   00  *   *
  
  Then in R:
  > library(Rsamtools)
  > blah = scanBam("foo.bam", param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = TRUE)))[[1]]
  > blah$qname
  [1] "000000F|arrow"
  > blah = scanBam("foo.bam", param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = FALSE)))[[1]]
  > blah$qname
  character(0)
  
  
original_text: 1075: <p>I have this read in my BAM file. It maps on chromosome 1.</p>
  
  <p>I open this BAM file in IGV, and I can see the alignment on chromosome 1.</p>
  
  <p>But when I open this file in R with Rsamtools:</p>
  
  <pre><code>bamContigsCel &lt;- Rsamtools::scanBam('output/alignment/pacbio/bwa/ref     /bristolAssemblySorted.bam', param = Rsamtools::ScanBamParam(what = Rsamtools::scanBamWhat(), flag = Rsamtools::scanBamFlag(isMinusStrand = FALSE), tag = bamTags))[[1]]
  </code></pre>
  
  <p>I then check if the read maps to chromosome 1 in my R object but I cannot find it.</p>
  
  <pre><code>bamContigsCel$rname[bamContigsCel$qname == '000000F|arrow']
  [1] II II IV
  Levels: I II III IV MtDNA V X
  </code></pre>
  
  <p>But if I look at the BAM file, it's there. Why isn't Rsamtools importing my read into R?</p>
  
  <pre><code>$ samtools view bristolAssemblySorted.bam | grep -n '000000F' | head  -c80
  000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   0 0   GAAGCTGTCTAAACTTTGGC
  </code></pre>
  
  <p>Cross-posted on <a href="https://www.biostars.org/p/261365/" rel="noreferrer">biostars</a></p>
   77: <p>Note the flag; that read is mapped in a reverse-complemented manner, so <code>isMinusStrand = FALSE</code> is filtering it out. I tested this by making a BAM file with only that read:</p>
  
  <pre><code>@SQ SN:I    LN:1000000
  000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   00  *   *
  </code></pre>
  
  <p>Then in R:</p>
  
  <pre><code>&gt; library(Rsamtools)
  &gt; blah = scanBam("foo.bam", param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = TRUE)))[[1]]
  &gt; blah$qname
  [1] "000000F|arrow"
  &gt; blah = scanBam("foo.bam", param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = FALSE)))[[1]]
  &gt; blah$qname
  character(0)
  </code></pre>
  