[maker-devel] Functional annotation options

[Mikael Brandström Durling]

26 feb 2014 kl. 10:43 skrev Mikael Brandström Durling <mikael.durling at slu.se<mailto:mikael.durling at slu.se>>:


26 feb 2014 kl. 09:26 skrev Marc Höppner <marc.hoeppner at imbim.uu.se<mailto:marc.hoeppner at imbim.uu.se>>:

Dear List,

I have finished a gene build now, and I would like to go over to functional annotation. I understand that maker includes a few script to facilitate such analyses. However, I have a few questions about this:

1) iprscan
It seems maker includes a MPI wrapper for InterProscan, but requests ‘iprscan’ to be in $PATH. The latest versions of Interproscan I have worked with are java applications and eventho I put their location in $PATH, mpi_iprscan seems to want something else? But what?

I don’t believe it works with interproscan5. What I usually do is to split the maker protein file into chunks, and then run these chunks as separate jobs on our cluster, then finally merge the results. The TSV file form iprscan5 can be input into the maker tool ipr_update_gff. I have not tried the iprscan2gff3, as I haven’t figured how to get an iprscan4 raw file from iprscan5.

I should clarify this and say that mpi_iprscan doesn’t seem to work with iprscan5. ipr_update_gff3 does, however.


Mikael

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