Body: <p>I recently finished mapping an RNAseq run using STAR2.3.0 and noticed the read1 and read2 counts are different, according to samtools flagstat. </p>
  
  <p>The map% is ~80% but the R1 R2 counts are:</p>
  
  <p>R1=139283692</p>
  
  <p>R2=137472495</p>
  
  <p>This usually does not happen for PE sequencing, which makes me a bit nervous to proceed with analysis. What are some potential reasons something like this could occur? I do not have experience with this happening and can't seem to find reasons by searching the web.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-17T18:59:16.737Z
Comments.Text: Presumably, the actual read counts in your two fastq source files are the same, right? I have no experience with RNAseq but the first thing that comes to mind is a problem in the sequencing step where too many reads were of low quality and were discarded by the aligner. Does that make sense?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-17T19:01:21.650Z
Comments.Text: The actual read counts of the two fastq source files are the same. It makes sense and was a thought of mine. I was wondering if there is a concrete way to check this out?
Comments.UserDisplayName: d_kennetz
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-18T12:32:35.643Z
Comments.Text: Use FastQC to compare the overall quality of both fastq files.
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-29T15:59:05.650Z
Comments.Text: @d_kennetz Does the actual read counts matches R1? Have you checked which of the reads are missing in the bam file?
Comments.UserDisplayName: Kamil S Jaron
Tags: <rna-seq><illumina><star>
Title: What could cause differing counts of R1 and R2 in Paired End Sequencing (RNASEQ)
ThreadText: # What could cause differing counts of R1 and R2 in Paired End Sequencing (RNASEQ)
  
  (Asked by: username_0 on 2019-04-17)
  
  I recently finished mapping an RNAseq run using STAR2.3.0 and noticed the read1 and read2 counts are different, according to samtools flagstat.
  
  The map% is ~80% but the R1 R2 counts are:
  
  R1=139283692
  
  R2=137472495
  
  This usually does not happen for PE sequencing, which makes me a bit nervous to proceed with analysis. What are some potential reasons something like this could occur? I do not have experience with this happening and can't seem to find reasons by searching the web.
  
  **Tags:** rna-seq, illumina, star
  
  > **Comments:**
  > **username_1**: Presumably, the actual read counts in your two fastq source files are the same, right? I have no experience with RNAseq but the first thing that comes to mind is a problem in the sequencing step where too many reads were of low quality and were discarded by the aligner. Does that make sense?  
  > **username_0**: The actual read counts of the two fastq source files are the same. It makes sense and was a thought of mine. I was wondering if there is a concrete way to check this out?  
  > **username_2**: Use FastQC to compare the overall quality of both fastq files.  
  > **username_3**: @username_0 Does the actual read counts matches R1? Have you checked which of the reads are missing in the bam file?  
  
  ---
  
  ## 0 answers
  
  