Ditching full genomes, using hematodinium transcriptomev1.6

Using NCBI Genomes Here were my planned steps last time: BLASTx of transcriptome 2.0 against the protein sequences from the C. opilio genome downloaded from NCBI BLASTn of transcriptome 2.0 against the Amoebophrya sp. genome downloaded from NCBI Use those two BLAST results to determine which genes are Hematodinium in origin and which are C. bairdi for all of Transcriptome 2.0 I completed all steps (plus a few tBLASTx of transcriptome 2.0 against Amoebophrya genome), but ran into a major problem. Specifically, not enough of our sequences are finding matches – after combining all matches for the C. opilio and Amoebophrya sp. genomes, only around half were matched, even after dropping the e-value bar all the way down to 10^-2 (and that’s with double-counting all sequences that matched to both genomes!). Link to all scripts and the specific numbers of matches available here So what now? Well, we’re still trying…

from Aidan F. Coyle https://ift.tt/3lmdWDG