ntamas
commented
8 years ago Hello,
I have checked the InterProScan output format here and it seems like not much has changed in the TSV format so I'm leaning towards saying that the output format of InterProScan 5 should be suitable for GFam. However, I cannot tell it for sure without seeing some test data on which I could run GFam and check the output. Can you upload some test data somewhere along with your GFam config file so I could try running the same thing on my machine?
yjx1217
Hello Tamás,
I tried gfam for my project to group cerevisiae reference proteome into gene families. It ran smoothly but I found the final results looked a bit confusing to me. 1) Many functional annotation generated by Interproscan (e.g. those Panther annotations shown in the domain_architecture.tab file ) was discarded in the final assigned_labels.txt file. So the annotation information in the assigned_labels.txt is quite sparse. 2) I didn't see how genes were grouped into gene families as I expected. Where could I find this information?
Since there is a major updates from interproscan4 to interproscan5 (even for the output format of interproscan), I was wondering if this could be a reason. I can provide test data if needed. Thanks in advance!