Using NCBI Genomes

Transcriptome 2.1 update… Last time I mentioned potentially using Sam’s transcriptomes created by taking cbai_transcriptome_v2.0 and filtering Alveolata and non-_Alveolata_ by taxa, thus producing cbai_transcriptome_v2.1 and hemat_transcriptome_v2.1. However, when I downloaded those two transcriptomes, they had ~230,000 and ~30,000 sequences respectively – far less than the ~1.4 million found in cbai_transcriptome_v2.0. Therefore, for the time being, we are neglecting this alternative route. Alright, on to my main update! Last time.. In my last post, I characterized the method of choice for obtaining taxa information. The plan was to do the following: Download all Alveolata and Arthropoda nucleotide sequences from the NCBI database, available from the NCBI Taxonomy Browser Obtain a FASTA file of all DEGs for our two meaningful conditions – elev day 2 vs. amb. day 2, and elev day 0 vs. elev day 2 – by cross-referencing transcript IDs and transcriptome 2.0 BLASTn those obtained FASTA files twice…

from Aidan F. Coyle