Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018, 2019, 2020-GW, 2020-UW) and cbai_transcriptome_v3.0 (RNAseq shorthand: 2018, 2019, 2020-UW). Both of these transcriptomes were assembled without any taxonomic filter applied. DIAMOND BLASTx and conversion to MEGAN6 RMA6 files was performed yesterday (20200604).
Will import RMA6 files into MEGAN6 and extract all non_Alveolata (dinoflagellates) sequences to create new transcriptomes. The new transcriptomes will be named cbai_transcriptome_v2.1 and cbai_transcriptome_v3.1. I’ll also extract only Alveolata sequences to generate a Hematodinium sp. transcriptome.
RESULTS
Output folder:
C.bairdi Transcritpomes:
cbai_transcriptome_v2.1.fasta (241MB)
cbai_transcriptome_v3.1.fasta (139MB)
Hematodinium sp. Transcriptomes:
Screenshots of taxonomic trees in MEGAN6 used to extract sequences for each new transcriptome:
cbai_transcriptome_v2.0 MEGAN non-Alveolota taxonomic tree
cbai_transcriptome_v3.0 MEGAN non-Alveolota taxonomic tree
hemat_transcriptome_v2.0 MEGAN Alveolata only taxonomic tree
hemat_transcriptome_v3.0 MEGAN Alveolata only taxonomic tree
The transcriptomes will be added to our Genomic Resources wiki. Next up is to run BUSCO and generate BUSCO comparisons to previous transcriptome assemblies.