DDrabeck

hmmm ok maybe this is a data issue... So my proteins.fa file has output: >MBRI_000001-T1 MBRI_000001 Which I would need to look like this >MBRI_000001-T1 gene:MBRI_000001 But in doing a...

I see, so my thought was that if I extracted a file that was like this: >MBRI001-T1 MBRI001 PTCHD1_1 JHDFLKJSDFLKJSDFH then I might see many funannotate genes with the same...

While I still am hoping to get a file that is uniform with NCBI format I'm gathering that perhaps submitting these to NCBI with the funannotate output will generate the...

(From just a cursory glance it seems that all the individual locus tags have one RNA each, which makes sense why there would then be only one transcript per gene...

> Ah so (and maybe this doesn't matter after all given that there are not actually isoforms in this data as I had originally thought) **If I wget from NCBI...

> * It depends on how close your comparison species are. > * Are you masking repeats well, TEs can often show up as species-specific genes and will be high...

Thank you both for this! It helps tremendously to clarify how these are called and the various things i need to be aware of in using this data!! On Tue,...

Hi--- just checking in here as I haven't heard back about this signal IP error issue.

I don't see an output for signalP at all. I re-ran it with a shell that specified module load signalp/5.0 The only log file it wrote was for phobius. This...

Gah! this made me realize there was a private group for the signalP module that I was not added to and was preventing me from using it/loading it properly! Sorry...