text: user2008: I'm currently trying to run bwa-mem on Influenza substrains using the following command: 
  ~/bwa mem h5n1_1_cons.fa h5n1_1_read1.fq h5n1_1_read2.fq
  
  h5n1_1_cons.fa is the consensus sequence for substrain h5n1_1, and the fq files are paired end reads 1 and 2. Running the program gives me this error: 
  [mem_sam_pe] paired reads have different names: "JQ714243-920-1", "JQ714243-920-2"
  
  Visual inspection shows that the read names are identical until the last character. I have found a package (bbmap) with a utility, bbrename.sh, that renames the sequences, producing:
  ./bbrename.sh in=h5n1_1_read1.fq out=fixed prefix=h5n1_1
  
  which yields the following output
  -bash-4.2$ head fixh5n1_1_read1.fq
  @h5n1_0
  gaaaatgtctcaggagttgatgcatggtgtttaatctttggtttgcgctg
  +
  @4>C5?7FA?9@@@;1,-4B+E??4E9,DA>6CB)*2.)?7/.'65+75/
  @h5n1_1
  catcagttggattttgcctaaggatgtccaccatccttatcccaccaatt
  +
  7(9?)=C3AEF+@@F=C-E>EE57CD:;'?.*?7;>:3>2.;29..)=2'
  @h5n1_2
  catgcatttgttggaataatgttctcacaaatcaactgtattgaccgctg
  
  This fixes the problem and allows BWA-MEM to work. However, header information is discarded. Is there another way to ensure the header names are the same while retaining all header information?
  
  user77: Assuming the read name lines only contain things like @JQ714243-920-1 and nothing else, then sed -i '1~4 s/-[12]$//' file.fastq (N.B., example updated a bit for safety, thanks to @terdon) will remove the -1 and -2 suffixes.
  However, you should try to figure out why the read names were munged into that form to begin with (at least Illumina machines won't produce that, I don't know about others).
  
original_text: 2008: <p>I'm currently trying to run bwa-mem on Influenza substrains using the following command: </p>
  
  <pre><code>~/bwa mem h5n1_1_cons.fa h5n1_1_read1.fq h5n1_1_read2.fq
  </code></pre>
  
  <p>h5n1_1_cons.fa is the consensus sequence for substrain h5n1_1, and the fq files are paired end reads 1 and 2. Running the program gives me this error: </p>
  
  <pre><code>[mem_sam_pe] paired reads have different names: "JQ714243-920-1", "JQ714243-920-2"
  </code></pre>
  
  <p>Visual inspection shows that the read names are identical until the last character. I have found a package (bbmap) with a utility, bbrename.sh, that renames the sequences, producing:</p>
  
  <pre><code>./bbrename.sh in=h5n1_1_read1.fq out=fixed prefix=h5n1_1
  </code></pre>
  
  <p>which yields the following output</p>
  
  <pre><code>-bash-4.2$ head fixh5n1_1_read1.fq
  @h5n1_0
  gaaaatgtctcaggagttgatgcatggtgtttaatctttggtttgcgctg
  +
  @4&gt;C5?7FA?9@@@;1,-4B+E??4E9,DA&gt;6CB)*2.)?7/.'65+75/
  @h5n1_1
  catcagttggattttgcctaaggatgtccaccatccttatcccaccaatt
  +
  7(9?)=C3AEF+@@F=C-E&gt;EE57CD:;'?.*?7;&gt;:3&gt;2.;29..)=2'
  @h5n1_2
  catgcatttgttggaataatgttctcacaaatcaactgtattgaccgctg
  </code></pre>
  
  <p>This fixes the problem and allows BWA-MEM to work. However, header information is discarded. Is there another way to ensure the header names are the same while retaining all header information?</p>
   77: <p>Assuming the read name lines only contain things like <code>@JQ714243-920-1</code> and nothing else, then <code>sed -i '1~4 s/-[12]$//' file.fastq</code> (N.B., example updated a bit for safety, thanks to @terdon) will remove the <code>-1</code> and <code>-2</code> suffixes.</p>
  
  <p>However, you should try to figure out <strong>why</strong> the read names were munged into that form to begin with (at least Illumina machines won't produce that, I don't know about others).</p>
  