Many reads from a recent RNA-seq sequencing run I had done are not mapping to the reference sequence they had come from. I converted some of the sequences to fasta format, and blasted them against NR allowing everything, and indeed the few that I have looked at appear to be on a whole different part of the phylogenetic tree than the organism I was going for.
The problem is that right now, using NCBI Blast, I can view a tree of results for a single sequence in my list of hundreds that I wanted to test. Is there a way to view a tree of hundreds of results? What I had in mind was maybe just pulling the top 5 hits from each of the 100 results, and adding those to a phylogenetic tree, along with counts on how many times each species showed up in the list.
Of course this is just an idea. What I really want to answer is "what is this stuff?". So any ideas you have for visualizing blast results on a subset of my unmapped reads would be much appreciated.
Thanks for your time!