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!