Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-07T18:51:26.807Z
Answers.LastActivityDate: 2018-08-07T18:51:26.807Z
Answers.UserDisplayName: Matt Bashton
Body: <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>
  
Tags: <rna-seq><salmon>
Title: Where to get '--fldMean' and '--fldSD' for single-end Salmon run
ThreadText: # Where to get '--fldMean' and '--fldSD' for single-end Salmon run
  
  (Asked by: username_0 on 2018-08-07)
  
  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?
  
  **Tags:** rna-seq, salmon
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-08-07. Score: 1 | Accepted answer
  
  From looking at the salmon documentation [here](http://salmon.readthedocs.io/en/latest/salmon.html#using-salmon), 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](https://github.com/COMBINE-lab/salmon/issues/127) 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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351865/) stage which you have sequenced (in part) on your sequencer. Thus ideally this sort of data should come from a [bioanalyzer](https://web.uri.edu/gsc/agilent-2100-bioanalyzer/) trace from whoever performed the library prep or similar QC step, this should ideally show the mean fragment length and standard deviation.
  
  
  ---
  
  