Index of /EvidentialGene/arthropods/triboliumbeetle/othergenes/tcas4

 Name                        Last modified       Size  

 Parent Directory            24-Dec-2014 17:24      -  
 tribcas_tcas4aug.aa.gz      06-Dec-2014 13:57   5.2M  
 tribcas_tcas4aug.aa.qual    06-Dec-2014 13:58   659k  
 tribcas_tcas4aug.aaid.tab   11-Dec-2014 14:51   1.5M  
 tribcas_tcas4aug.mrna.count 11-Dec-2014 15:24   855k  
 tribcas_tcas4aug.mrna.gz    11-Dec-2014 15:15  11.7M  

Data source
http://bioinf.uni-greifswald.de/tcas/index.html
http://bioinf.uni-greifswald.de/tcas/genes/annotation
Annotation of T. castaneum based on Assembly 4.0 submitted to GenBank (status pending).
      Tcas4.genbank.gff3.gz: gff file 
      Tcas4.0_annotation.aa: protein fasta file 
      Tcas4.0_annotation.mrna: mRNA fasta file 

--------------
Data source RNA-seq from 
BMC Genomics. 2014; 15(1): 445.
Published online Jun 7, 2014. doi:  10.1186/1471-2164-15-445
Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis

Two pops of Tcas beetle, 3 repl, 2Bill paired reads .. only using genome-mapped reads..
Tcas v4 genome asm in progress, w/ Tcas v4 gene set by M. Stanke et al., Augustus models

SRA
 grep SRP033773 sra_rnaseq2_201411.csv | grep 'Replicate 2' | perl -ne 's/","/\t/g; s/"//g; @v=split"\t"; ($sp,$ns)=@v[2,11]; $ns{$sp}+=$ns; $n++; print join("\t",@v[0,1,2],sprintf"%.1f",$ns/$M)."\n"; END{ for $sp (sort keys %ns) { $c=$ns{$sp}; $cm=sprintf"%.1f",$c/$M; print join("\t",sprintf("%27s",$sp),$n,$cm,$ns{$sp})."\n"; } }BEGIN{$M=1000000;} ' | head -20

SRX391109	SB 18 hours naive control, Replicate 2	Tribolium castaneum	27.9
SRX391098	SB six hours naive control, Replicate 2	Tribolium castaneum	29.6
SRX391093	Cro1 18 hours naive control, Replicate 2	Tribolium castaneum	29.8
SRX391086	Cro1 six hours naive control, Replicate 2	Tribolium castaneum	35.6
SRX390658	SB 18 hours pricking control, Replicate 2	Tribolium castaneum	26.0
SRX390656	SB six hours pricking control, Replicate 2	Tribolium castaneum	29.5
SRX390653	Cro1 18 hours after pricking infection, Replicate 2	Tribolium castaneum	26.1
SRX390650	Cro1 18 hours after oral infection, Replicate 2	Tribolium castaneum	31.3
SRX390646	Cro1 18 hours pricking control, Replicate 2	Tribolium castaneum	32.9
SRX390643	Cro1 six hours pricking control, Replicate 2	Tribolium castaneum	32.8
SRX390638	SB 18 hours after pricking infection, Replicate 2	Tribolium castaneum	35.6
SRX390635	SB six hours after pricking infection, Replicate 2	Tribolium castaneum	25.9
SRX390632	SB 18 hours after oral infection, Replicate 2	Tribolium castaneum	32.9
SRX390629	SB six hours after oral infection, Replicate 2	Tribolium castaneum	29.9
SRX390626	Cro1 six hours after pricking infection, Replicate 2	Tribolium castaneum	24.5
SRX390600	Cro1 six hours after oral infection, Replicate 2	Tribolium castaneum	42.2

all 3 reps, 48 SRX entries, 1.5 Bill pairs (3 bill reads, 100bp)