Answers.Body: <p>Bam files contain a MAPQ field that informs on whether an alignment is unique or not. With STAR, a MAPQ value of 255 means the read is mapped uniquely and a score lower than 255 means not unique.</p>
  <p>You can use samtools on a bam file to count or output the uniquely or multimapped reads by filtering for the MAPQ as described here: <a href="https://groups.google.com/forum/#!topic/rna-star/ipHc9FrgaPU" rel="nofollow noreferrer">https://groups.google.com/forum/#!topic/rna-star/ipHc9FrgaPU</a></p>
  <p>For example, count uniquely mapped reads:
  <code>samtools view -c -q 255 myBamFile.bam</code><br />
  Output uniquely mapped reads:
  <code>samtools view -q 255 myBamFile.bam</code></p>
  <p>There are differences between STAR and BWA MAPQ output though. see here for details: <a href="https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/" rel="nofollow noreferrer">https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-20T03:03:23.467Z
Answers.LastActivityDate: 2022-02-20T03:14:18.773Z
Answers.LastEditDate: 2022-02-20T03:14:18.773Z
Answers.UserDisplayName: Robert ietswaart
Body: <p>I want to find and compare the results from STAR and BWA- MEM mapped. I have 150bp paired end reads in sorted.bam files in each case and i want to find in each case uniquely mapped reads, number of reads mapped to multiple loci and number of unmappped reads.</p>
  <p>Especially for uniquely mapped reads i tried different solutions from biostars and this <a href="https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment">Obtaining uniquely mapped reads from BWA mem alignment</a> but i dont know what to trust,</p>
  <p>Could you please suggest the best way to find mapping results from bam paired end files ?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T14:22:29.687Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T14:28:28.687Z
Comments.Text: It would be helpful to describe the genome and a bit of project background regarding what you have already tried. Biostars is a different site to Stackexchange.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T15:08:09.557Z
Comments.Text: I have paired end mapped reads from human in sorted bam files and i want to find the unique mapped , the multimapped and the unmapped reads from BWA and from STAR. I already have the .bam files from each mapper. i Tried samtools flagstat and the solution above but i am not sure if this is correct especially for unique reads
Comments.UserDisplayName: user3683485
Tags: <linux><bwa><star>
Title: Compare mapped reads from BWA -MEM and STAR from .bam files
ThreadText: # Compare mapped reads from BWA -MEM and STAR from .bam files
  
  (Asked by: username_0 on 2022-02-14)
  
  I want to find and compare the results from STAR and BWA- MEM mapped. I have 150bp paired end reads in sorted.bam files in each case and i want to find in each case uniquely mapped reads, number of reads mapped to multiple loci and number of unmappped reads.
  
  Especially for uniquely mapped reads i tried different solutions from biostars and this [Obtaining uniquely mapped reads from BWA mem alignment](https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment) but i dont know what to trust,
  
  Could you please suggest the best way to find mapping results from bam paired end files ?
  
  **Tags:** linux, bwa, star
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: It would be helpful to describe the genome and a bit of project background regarding what you have already tried. Biostars is a different site to Stackexchange.  
  > **username_0**: I have paired end mapped reads from human in sorted bam files and i want to find the unique mapped , the multimapped and the unmapped reads from BWA and from STAR. I already have the .bam files from each mapper. i Tried samtools flagstat and the solution above but i am not sure if this is correct especially for unique reads  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-02-20. Score: 2
  
  Bam files contain a MAPQ field that informs on whether an alignment is unique or not. With STAR, a MAPQ value of 255 means the read is mapped uniquely and a score lower than 255 means not unique.
  
  You can use samtools on a bam file to count or output the uniquely or multimapped reads by filtering for the MAPQ as described here: <https://groups.google.com/forum/#!topic/rna-star/ipHc9FrgaPU>
  
  For example, count uniquely mapped reads:
  `samtools view -c -q 255 myBamFile.bam`  
  Output uniquely mapped reads:
  `samtools view -q 255 myBamFile.bam`
  
  There are differences between STAR and BWA MAPQ output though. see here for details: <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>
  
  
  ---
  
  