text: user2005: I need to run single-end bulk-RNAseq salmon - based alignment and I am not sure what I should supply as --fldMean and --fldSD which seem to be crucial for the single-end experiment alignment. Can they be somehow derived from the FASTQ files that I have, or should I be provided with them by someone who did the experiment?
  
  user1769: From looking at the salmon documentation here, it is correct that both of these are essential for single end experiments:
  
  Since the empirical fragment length distribution cannot be estimated from the mappings of single-end reads
  
  From the discussion here it would appear that you can't estimate these parameters at all via the FASTQ files alone.
  The fragment length refers to the physical molecule of D/RNA captured in the library prep stage which you have sequenced (in part) on your sequencer.  Thus ideally this sort of data should come from a bioanalyzer trace from whoever performed the library prep or similar QC step, this should ideally show the mean fragment length and standard deviation. 
  
original_text: 2005: <p>I need to run <code>single-end</code> <code>bulk-RNAseq</code> <code>salmon</code> - based alignment and I am not sure what I should supply as <code>--fldMean</code> and <code>--fldSD</code> which seem to be crucial for the <code>single-end</code> experiment alignment. Can they be somehow derived from the <code>FASTQ</code> files that I have, or should I be provided with them by someone who did the experiment?</p>
   1769: <p>From looking at the salmon documentation <a href="http://salmon.readthedocs.io/en/latest/salmon.html#using-salmon" rel="nofollow noreferrer">here</a>, it is correct that both of these are essential for single end experiments:</p>
  
  <blockquote>
    <p>Since the empirical fragment length distribution cannot be estimated from the mappings of single-end reads</p>
  </blockquote>
  
  <p>From the discussion <a href="https://github.com/COMBINE-lab/salmon/issues/127" rel="nofollow noreferrer">here</a> it would appear that you can't estimate these parameters at all via the FASTQ files alone.</p>
  
  <p>The fragment length refers to the physical molecule of D/RNA captured in the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351865/" rel="nofollow noreferrer">library prep</a> stage which you have sequenced (in part) on your sequencer.  Thus ideally this sort of data should come from a <a href="https://web.uri.edu/gsc/agilent-2100-bioanalyzer/" rel="nofollow noreferrer">bioanalyzer</a> trace from whoever performed the library prep or similar QC step, this should ideally show the mean fragment length and standard deviation. </p>
  