natir
commented
5 months ago Hello,
If you don't specify minimum abundance values, br will attempt to determine it on its own. There are 4 methods based on the kmer count histogram:
- first-minimum: br chooses the minimum abundance corresponding to the first minimum in the kmer count histogram
- rarefaction: br chooses the minimum abundance corresponding to the elimination of a certain number of kmer.
- percent-most: Remove at most n percent of total kmer
- percent-least: Remove at least n percent of total kmer
If the first-minimum method failed to determine a minimum abundance, it's probably because the reads have too many errors and don't correspond to a classic curve. https://www.researchgate.net/figure/K-mer-histogram-The-x-axis-refers-to-the-k-mer-depth-Dk-which-indicates_fig4_309161336
You can choose the minimum abundance yourself or try another method.
(Sorry br isn't release ready)
Attempting to run br on a 15 Gb dataset of reads > 10kb with parameters:
br -k 19 -i STL_F2_isoline_pooled.10k.fa -o brutal-out -t 32It gives the error, "Error: Can't compute minimal abundance". Do you have a suggestion for a default to supply?