Hi guys, I wanted to use Bandage to visualize some transcripts from my Trinity assembly. I realised that when I search for nodes, only fragments that correspond to gene 1 from the contig are present, but never for genes 2,3 etc. To explain more clearly - I have a transcript with the following name:
>TRINITY_DN35682_c0_g1_i2 len=790 path=[0:0-704 1:705-789]
When I search for this node in Bandage I type 35682_c0_0 and I see a graph corresponding to my transcript. But when I look for another gene from the same contig I can't find it. It is:
>TRINITY_DN35682_c0_g2_i1 len=736 path=[0:0-735]
I was also typing 35682_c0_0 since it is the same contig. Should I have searched for something else?
Also, when I zoom out I don't see anything similar in the proximity of the gene 1 graph although these two transcripts are next to each other in my Trinity.fasta file.
I also checked if that is happening for other contigs with multiple genes, and the problem remains.
