[BioC] How to get all transcripts

[Petr [guest]]

Dear Igoff,

I have a trouble to understand some value in cummeRbund - I am sorry for disturbing, but I did not find any answer on Internet.

I have two mouses paired-end sequenced. I mapped with Tophat2 - make Cufflinks - and Cufdiff (one replicates - two conditions) - and CummeRbund. It is very nice graphs and outputs, but I would like to get just one number, which tell me total transcript expression for mouse1 and for mouse2 and compare it.

It is possible to take output form Cufflinks - transcripts.gtf and extract FPKM value for all genes and do sum of all FPKM's?  Something like - awk 'OFS="t"{sum+=$16}END {print sum}' transcripts.gtf.

And also when I print in R command replicates(cuff) - what does it mean value total_mass, norm_mass and internal_scale? Can I use value total_mass to explain differences between transcripts?

Are those values somewhere detailed explained?

Thank you so much for any help - I am little desperate :-(

Kind Regards,

Petr.

 -- output of sessionInfo(): 

> session(info)
Error: could not find function "session"
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] cummeRbund_2.5.3      Gviz_1.7.10           rtracklayer_1.23.22  
 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30  IRanges_1.21.44      
 [7] fastcluster_1.1.13    reshape2_1.2.2        ggplot2_0.9.3.1      
[10] RSQLite_0.11.4        DBI_0.2-7             BiocGenerics_0.9.3   

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.25.17     BatchJobs_1.2            
 [3] BBmisc_1.5                Biobase_2.23.6           
 [5] BiocParallel_0.5.20       biomaRt_2.19.3           
 [7] Biostrings_2.31.22        biovizBase_1.11.15       
 [9] bitops_1.0-6              brew_1.0-6               
[11] BSgenome_1.31.13          cluster_1.15.2           
[13] codetools_0.2-8           colorspace_1.2-4         
[15] dichromat_2.0-0           digest_0.6.4             
[17] fail_1.2                  foreach_1.4.1            
[19] Formula_1.1-1             GenomicAlignments_0.99.38
[21] GenomicFeatures_1.15.15   gtable_0.1.2             
[23] Hmisc_3.14-3              iterators_1.0.6          
[25] labeling_0.2              lattice_0.20-29          
[27] latticeExtra_0.6-26       MASS_7.3-31              
[29] matrixStats_0.8.14        munsell_0.4.2            
[31] plyr_1.8.1                proto_0.3-10             
[33] RColorBrewer_1.0-5        Rcpp_0.11.1              
[35] RCurl_1.95-4.1            R.methodsS3_1.6.1        
[37] Rsamtools_1.15.41         scales_0.2.3             
[39] sendmailR_1.1-2           splines_3.1.0            
[41] stats4_3.1.0              stringr_0.6.2            
[43] survival_2.37-7           tools_3.1.0              
[45] VariantAnnotation_1.9.49  XML_3.98-1.1             
[47] XVector_0.3.7             zlibbioc_1.9.0           
> 


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