I have a pooled RNA seq data from 5 to 10 individuals at different stages. I want to assemble them and combine all of data as one big fastq files. I use the bbnorm to reduce the replicates. But I have a question about how to set the parameters as:
target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread
Because I have the pooled data, how can I set the mindepth and minkmers for the following analysis? I need some suggestions on how to reduce the reads with error and also keep the isoform.