I am trying to view the results of an all vs all blastp of some sequences with cytoscape.
I've been using the Blast2SimilarityGraph app to read in my data (blast -m 8 + fasta file) and then a few other apps to do what i want. This works fine.
However my problem is that Blast2SimilarityGraph does not work for larger files (>~19,000 seqs). I am not sure why,It is not a memory issue as i am using quite a powerful box, it seems more likely to be a default limit.
Does any have any suggestions for a better way to read in my files or an alternative app?
Appreciate your time guys