Index of /EvidentialGene/arthropods/whiteshrimp/litova1version1

 Name                     Last modified       Size  

 Parent Directory         10-Jun-2013 15:37      -  
 scripts/                 05-Dec-2012 18:13      -  
 whiteshrimp-sralist.txt  05-Dec-2012 17:59     1k  
 whiteshrimp1best.aa.gz   17-Nov-2012 13:31  12.5M  
 whiteshrimp1best.aa.qual 05-Dec-2012 14:33   5.4M  
 whiteshrimp1best.tr.gz   05-Dec-2012 18:07  22.7M  
 whiteshrimp_readme.txt   05-Dec-2012 18:18     1k  

Pacific white shrimp transcriptome assembled with EvidentialGene methods

arthropods.eugenes.org/EvidentialGene/whiteshrimp/
2012 oct, Don Gilbert, gilbertd near indiana edu

RNA-Seq Data:
NCBI BioProject:PRJNA73443  Litopenaeus vannamei transcriptome sequencing (SRP008317)
see sralist.txt

Assembly:
diginorm.sh  :  redunancy filter reads with digital normalization by kmer, using khmer package, 2012 Sept
velrun*.sh   : Velvet/Oases, multi-kmer assembly, versions current as of 2012 July
processtr.sh : Protein finding, best protein/transcript selection
  using evigene/cdna_bestorf, cd-hit, scripts

Summary
whiteshrimp1best:  Total ntr= 111090 (many are poor, to be filtered, below)
whiteshrimp longest 1k aa:

                aa1k    trlen   aafull  utrok   aarange       
whishrimp1vel12 1723    6532    78      92      1081,1421,8754   # litova_vel1vel3.cd90
whishrimp1tri   1281    4356    51      97      823,1090,5854    # litova1tri1.all_cd
whishrimp0tsa   722     2351    29      99      516,657,2502     # litova0tsa.all_cd

#...................
FIXME: separate these 150k aa,tr into good, poor subsets
  good: 1. included in orthomcl groups; bugs/omclbugs10/omcl10a1_all/bug10a_omclgn.tab, 50k
        2. else, >=60aa? and complete, or >=120aa and partial
    == 70k ?
  poor: remainder, mostly partial, under 60 aa