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Index of /EvidentialGene/plants/arabidopsis

      Name                     Last modified       Size  

[DIR] Parent Directory 21-May-2017 19:09 - [DIR] evigene_tr2aacds_test/ 20-May-2013 13:16 - [DIR] evigene2017_arabidopsis/ 22-May-2017 20:28 -


evigene2017_arabidopsis
-----------------------
Arabidopsis Gene Assembly from RNA-seq with EvidentialGene methods,
and comparison to Pac-Bio RNA, and genome modeled gene sets.
This is a reference-free gene set (no external data was used to make gene assemblies)
and has value for that (i.e. no errors from other sources complicate these genes).

evigene_tr2aacds_test
---------------------
Test case for EvidentialGene_trassembly_pipe (evigene/scripts/prot/tr2aacds.pl)
   http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html

TEST RUN THIS outside of PBS/qsub cluster to see if it works:
  env trset=arath_TAIR10_20101214up.cdna.gz datad=`pwd` ./tr2aacds_test.sh > & log.tr2ac1

NOTE: You need to edit the app paths in tr2aacds_test.sh for your system.

TEST DATA: arabidopsis TAIR10 transcripts (headers regularized, though probably not needed)
  curl -sR -o arath_TAIR10_20101214up.cdna \
    ftp://ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated

Get also TAIR10_pep and TAIR10_cds to compare w/ evigene output
This takes 20 min to run on 2 cores of intel game box 


Developed at the Genome Informatics Lab of Indiana University Biology Department