text: user2477: Which Read Groups are correct:
  java -Xmx4G -jar picard.jar AddOrReplaceReadGroups \
  I=$SNIC_TMP/WCRO84_S23_L005.bam \
  O=WCRO84_S23_L005.bam \
  RGID=WCRO84_S23_L005 \
  RGLB=WCRO84 \
  RGPL=illumina \
  RGPU=WCRO84_S23_L005 \
  RGSM=WCRO84
  
  or
  java -Xmx4G -jar picard.jar AddOrReplaceReadGroups \
  I=$SNIC_TMP/WCRO84_S23_L005.bam \
  O=WCRO84_S23_L005.bam \
  RGID=WCRO84_S23_L005 \
  RGLB=WCRO84_S23_L005 \
  RGPL=illumina \
  RGPU=WCRO84_S23_L005 \
  RGSM=WCRO84_S23_L005
  
  Or is a better way to determine read groups?
  Thank you in advance,
  
  user77: Usually it doesn't actually matter, but if you want it to be very correct:
  RGID=SomeLibraryID \
  RGLB=SomeLibraryID \
  RGPL=illumina \
  RGPU=Some_Sequencer_ID \
  RGSM=SomeSampleID
  
  That assumes you have one library per sample and aren't splitting the output BAM files by lane.
  
original_text: 2477: <p>Which Read Groups are correct:</p>
  
  <pre><code>java -Xmx4G -jar picard.jar AddOrReplaceReadGroups \
  I=$SNIC_TMP/WCRO84_S23_L005.bam \
  O=WCRO84_S23_L005.bam \
  RGID=WCRO84_S23_L005 \
  RGLB=WCRO84 \
  RGPL=illumina \
  RGPU=WCRO84_S23_L005 \
  RGSM=WCRO84
  </code></pre>
  
  <p>or</p>
  
  <pre><code>java -Xmx4G -jar picard.jar AddOrReplaceReadGroups \
  I=$SNIC_TMP/WCRO84_S23_L005.bam \
  O=WCRO84_S23_L005.bam \
  RGID=WCRO84_S23_L005 \
  RGLB=WCRO84_S23_L005 \
  RGPL=illumina \
  RGPU=WCRO84_S23_L005 \
  RGSM=WCRO84_S23_L005
  </code></pre>
  
  <p>Or is a better way to determine read groups?</p>
  
  <p>Thank you in advance,</p>
   77: <p>Usually it doesn't actually matter, but if you want it to be very correct:</p>
  
  <pre><code>RGID=SomeLibraryID \
  RGLB=SomeLibraryID \
  RGPL=illumina \
  RGPU=Some_Sequencer_ID \
  RGSM=SomeSampleID
  </code></pre>
  
  <p>That assumes you have one library per sample and aren't splitting the output BAM files by lane.</p>
  