I ran a subset of Yaamini’s ocean chemistry samples on our T5 Excellence titrator (Mettler Toledo) at the beginning of April. The subset were samples taken from the beginning, middle, and end of the experiment. The rationale for this was to assess whether or not total alkalinity (TA) varied across the experiment. If there was little variation, then there’d likely be no need to run all of the samples. However, should there be temporal differences, then all samples should be processed.
Data analysis was performed in the following R Project:
Continuing to try to find the best kmer setting to work with SparseAssemlber after the last attempt failed due to a kmer size that was too large (k 131; which happens to be outside the max kmer size  for SparseAssembler), I re-ran SparseAssembler with an arbitrarily selected kmer size < 131 (picked k 111).
So, this time, I simply increased the maximum kmer size to 301 and left all other settings as default. I’m hoping this is large enough to produce a smooth curve, with a maximal value that can be determined from the output graph.
Well, the graph is closer to what we’d expect, in that it appears to reach a zenith, but after that plateau, we see a sharp dropoff, as opposed to a gradual dropoff that mirrors the left half. Not entirely sure what the implications for this are, but I’ll go ahead an run SparseAssembler using a kmer size of 131 and see how it goes.
After the last SparseAssembler assembly completed, I wanted to do another run with a different kmer size (last time was arbitrarily set at 101). However, I didn’t really know how to decide, particularly since this assembly consisted of mixed read lenghts (50bp and 100bp). So, I ran kmergenie on all of our geoduck (Panopea generosa) sequencing data in hopes of getting a kmer determination to apply to my next assembly.
This data estimates the best kmer size for this data to be 121.
However, based on the kmergenie documentation, this is likely to be inaccurate. This inaccuracy is based on the fact that our kmer graph should be concave. Our graph, instead, is only partial – we haven’t reached a kmer size where the number of kmers is decreasing.
As such, I’ll try re-running with a different maximum kmer settting (default max is 121).