Index of /EvidentialGene/arthropods/whiteshrimp/litova1version1
Name Last modified Size
Parent Directory 10-Jun-2013 15:37 -
whiteshrimp_readme.txt 05-Dec-2012 18:18 1k
scripts/ 05-Dec-2012 18:13 -
whiteshrimp1best.tr.gz 05-Dec-2012 18:07 22.7M
whiteshrimp-sralist.txt 05-Dec-2012 17:59 1k
whiteshrimp1best.aa.qual 05-Dec-2012 14:33 5.4M
whiteshrimp1best.aa.gz 17-Nov-2012 13:31 12.5M
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
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