Hi, 

 

I am trying out the pipeline published in Trapnell et als Nature
Protocols paper
<http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html> . I
am getting an error in cummeRbund when I try to create the cuff_data
object (under R_2.15, couldn't install on 2.13 or 2.14(?)). After the
first attempt to create the database the error occurs. When I rerun it
generates a CuffSet but with same parameters even if datasets are
different.

 

> cuff_data<-readCufflinks("bam_cuffDiff")

Creating database bam_cuffDiff/cuffData.db

Reading bam_cuffDiff/genes.fpkm_tracking

Checking samples table...

Populating samples table...

Writing genes table

Reshaping geneData table

Recasting

Writing geneData table

Error in sqliteExecStatement(con, statement, bind.data) : 

  RS-DBI driver: (unable to bind data for parameter ':status')

> cuff_data

Error: object 'bamCuff' not found

> cuff_data<-readCufflinks("bam_cuffDiff")

> bamCuff

CuffSet instance with:

         1 samples

         24493 genes

         0 isoforms

         0 TSS

         0 CDS

         0 promoters

         0 splicing

         0 relCDS

 

I have more than 1 sample (14 samples, divided into 2 groups). My
cuffdiff call seems ok to me(?):

 

cuffdiff -o bam_cuffDiff -b
/data/shared/genomes/UMD_3.1/Bos_taurus.UMD3.1.64.fa -p 12 -L
FertP,FertN -u ./merged_asm/merged.gtf
/BAM/E_1,./BAM/E_3,./BAM/E_4,./BAM/E_5,./BAM/E_7,./BAM/E_22,./BAM/E_25
/BAM/E_8,./BAM/E_11,./BAM/E_12,./BAM/E_13,./BAM/E_17,./BAM/E_18,./BAM/E
_21

 

The only other instance of this error
<http://rna-seqblog.com/data-analysis/protocol-differential-gene-and-tra
nscript-expression-analysis-of-rna-seq-experiments-with-tophat-and-cuffl
inks/>  (in comments) seems due to incorrect cuffdiff call. I have
linked to the BAM files here but tried without the link. Output is
generated in each case and gives same results.

 

I hope someone has some advice=)

 

Bruce.

 

> sessionInfo()

R version 2.15.0 (2012-03-30)

Platform: i386-pc-mingw32/i386 (32-bit)

 

locale:

[1] LC_COLLATE=English_Ireland.1252  LC_CTYPE=English_Ireland.1252   

[3] LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C                    

[5] LC_TIME=English_Ireland.1252    

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base


 

other attached packages:

[1] cummeRbund_1.2.0 reshape2_1.2.1   ggplot2_0.9.0    RSQLite_0.11.1  

[5] DBI_0.2-5       

 

loaded via a namespace (and not attached):

 [1] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2
grid_2.15.0       

 [5] MASS_7.3-17        memoise_0.1        munsell_0.3        plyr_1.7.1


 [9] proto_0.3-9.2      RColorBrewer_1.0-5 scales_0.2.0
stringr_0.6

 

Bruce Moran MSc.,
Walsh Fellowship PhD Candidate,
Systems Biology Group,
Animal Bioscience and Research Dept.,

Teagasc, Dunsany, Co. Meath, Ireland.

 

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