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?
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asked Aug 7, 2018 at 16:53
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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.
