There are several parameters you can use to affect the table fullness, such as using the prefilter or reducing the number of bits per cell, or manually specifying the -Xmx parameter. Can you post the command line you used, and the standard error log? And, if possible, attach a kmer frequency histogram (from the full dataset). Even when the table gets really full, the accuracy is generally quite high.
Also, quality-trimming and adapter-trimming the data before analyzing it can have a huge impact, because the vast majority of the kmers that get counted are error kmers rather than genomic kmers; so anything that reduces the number of errors and amount of non-genomic sequence will be beneficial.
Also, quality-trimming and adapter-trimming the data before analyzing it can have a huge impact, because the vast majority of the kmers that get counted are error kmers rather than genomic kmers; so anything that reduces the number of errors and amount of non-genomic sequence will be beneficial.
Comment