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Index of /EvidentialGene/plants/arabidopsis/evigene_tr2aacds_test

      Name                                   Last modified       Size  

[DIR] Parent Directory 21-May-2017 14:26 - [   ] arath_TAIR10_20101214up.cdna.gz 15-Apr-2013 14:03 24.2M [TXT] arath_TAIR10_20101214up.mainalt.tab 20-May-2013 13:11 624k [TXT] arath_TAIR10_20101214up.mrna2tsa.info 20-May-2013 13:17 1k [TXT] arath_TAIR10_20101214up.mrna2tsa.log 20-May-2013 13:18 2k [TXT] arath_TAIR10_20101214up.pubids 20-May-2013 13:11 1.4M [TXT] arath_TAIR10_20101214up.tr2aacds.log 15-Apr-2013 16:22 8k [TXT] arath_TAIR10_20101214up.trclass 15-Apr-2013 16:22 2.9M [TXT] arath_TAIR10_20101214up.tsadesc.cmt 20-May-2013 13:11 1k [TXT] arath_TAIR10_20101214up.tsamethods.cmt 20-May-2013 13:11 1k [TXT] arath_TAIR10_20101214up.tsasubmit.sbt 20-May-2013 13:11 1k [DIR] dropset/ 20-May-2013 12:10 - [DIR] inputset/ 15-Apr-2013 16:24 - [DIR] okayset/ 20-May-2013 13:11 - [DIR] tmpfiles/ 15-Apr-2013 16:25 - [   ] tr2aacds_test.sh 15-Apr-2013 16:02 2k

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 
#-----------------------------------------

Next step: make NCBI TSA submission.
  evgmrna2tsa.pl will process above tr2aacds okayset into files
  for NCBI TSA submit, make public IDs, mRNA annotation (given names from blastp),
  vector screening, end-gap trim,  and run 'tbl2asn'.

Partial run to make tables of public IDs and  main-alt pairings.
  $evigene/scripts/evgmrna2tsa.pl -runstep "pubids" -log \
   -idprefix ArathEGr -class arath_TAIR10_20101214up.trclass

Full run with vecscreen, tbl2asn:
   export vecscreen=/path/to/ncbic/bin/vecscreen; export tbl2asn=/path/to/ncbic/bin/tbl2asn 
   evgmrna2tsa.pl -runtbl2asn -class arath_TAIR10_20101214up.trclass

Developed at the Genome Informatics Lab of Indiana University Biology Department