[maker-devel] TACC lonestar and N50 value

[Van Hoeck Arne]

Dear MAKER developer,

We have a plant genome of about 450 Mbp with an N50 value of 20 kbp whereas only 3/4 (333 Mbp) are contigs longer than 10 kbp. CEGMA said that 87% of the genes were found, whereas 94 % were partial identified.  You said last time that contigs smaller than 10kbp are not ideal for annotating and preferable to throw them away. Does this mean that I lose all genes present in the small contigs? Or is there another way to annotate them? (is concatenating all the small contigs together with 500 N's between each contig an option?)

Besides, i could run succesfully Maker via iplant's atmoshpere. However, for my large genomes i registred myself at the TACC lonestar cluster but Dave C. replied that i won't be able to run on the TACC supercomputers without an allocation. He said that I need to contact my PI. With my loginID, i haven't any acces to the cluser via ssh since my permission was denied. Therefore, is it possible to use the TACC supercomputers to run MAKER?

Best regards
Arne


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