<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>

CC BY-SA 4.0
2018-08-07T18:51:26.807Z
2018-08-07T18:51:26.807Z
Matt Bashton
<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>

<rna-seq><salmon>
Where to get '--fldMean' and '--fldSD' for single-end Salmon run
# 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.


---

