Hi all!
I have several questions regarding the usage of Salmon. I am trying to quantify the reads coming from the repeated genome (this is centromeres, transposons, simple repeats, etc.). I wonder whether using Salmon is a feasible/good way of doing so. If it is, then a second question pops out; which is the following:
Some of the repeats are smaller than the default K-mer choice (31), therefore are excluded from the index. Can I lower the K-mer value even though my data has a fragment length of 75bp?
If you argue than this is not the most suitable approach, could you suggest a different way of achieving what I am currently trying to do?
Thanks all before hand!
Cheers,
Jordi
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If you have a database of repeats for your organism, you might want consider using either SalmonTE or TETranscripts
Is there, conceptually any downside for using the regular version?
Nothing obvious to me. It might be worth running salmonTE and salmon on the same dataset (using a set of retrotransposons as the reference) and see if the results differ substantively.