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Old 07-17-2012, 11:15 AM   #21
ftorri
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Hi, Loyal helped me out in solving this issue.

You have to use:
myIDs<-as.vector(myIDs$V1) with a upper case v.

And then check:
is.vector(myIDs)

It should be true this time.

Fed
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Old 07-17-2012, 11:17 AM   #22
ftorri
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Hi all, does anyone of you know how I can install the developmental version of cummerbund? I am not able to use a lot of utilities with the one I have. I followed the instruction, but still I get the stable version:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.7, ?biocLite for help
> biocLite("cummeRbund")

thanks,

Fed
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Old 07-17-2012, 01:18 PM   #23
lgoff
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Hi guys,
when you read in IDs using read.table, it creates a data.frame. you must point to the first column and from that create a vector:


myIDs<-read.table("genes_ids.txt")

myIDs<-myIDs[,1] # Will create a vector of the first column values or myIDs$V1 unless you have column headers and then you can use the name of the column instead of V1 (V1 is R's default value for the first column of a data.frame that doesn't have column names. It must be capitalized 'V1')

I recommend that you make sure myIDs is a vector and that it contains all of the IDs you are interested before using it for getGenes...

Cheers,
Loyal
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Old 07-17-2012, 01:22 PM   #24
lgoff
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Hi Fed...
To use the biocLite() installer, you must be running the development version of R (2.16.0). Otherwise, you can download the development version from the cummeRbund website:

http://compbio.mit.edu/cummeRbund/

And then install it from the command line as follows:

Code:
R CMD INSTALL cummeRbund_1.99.2.tgz

You may have to install a few additional dependancies to get it working correctly.

Cheers,
Loyal
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Old 07-24-2012, 08:51 PM   #25
scor
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Default cuff gene set - cummeRbund

Hi all
I am trying to create a cuff gene set (for use with cummerbund) from a list of gene names. I have read the gene names in as a vector. This step seems fine and I have confirmed the vector with 'is.vector'. I do not have gene_ids. When I use the getGenes function on the names vector I do not get a gene set.
I get "CuffGeneSet instance for genes character(0)"

It seems to me that you probably need the list of gene_ids and it is not sufficient to only have a list of gene names.
If anyone can help with advice on how to create a geneset without having a list of gene_ids I would be grateful.
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Old 07-24-2012, 09:08 PM   #26
scor
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Default cuff gene set - cummeRbund

My apologies - the problem was that my gene names were in lower case. I just needed to change the names to upper case and I have been able to create a gene set.
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Old 08-01-2012, 10:41 AM   #27
vyellapa
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I was going through the CummerBund manual and things were smooth until I hit this error.

Code:
> myGenes <- getGenes(cuff, myGeneIds)
Error in sqliteExecStatement(conn, statement, ...) : 
  RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
I have seen the same error on this post but could not a solution. How can I resolve this error?
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Old 08-02-2012, 04:26 AM   #28
lgoff
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This happens in earlier versions of cummeRbund when a call to the database failed, subsequent calls would generate this error message. You can always re-connect to the database with:

cuff<-readCufflinks()

and this should alleviate the error. I will try to address this better in future versions

Cheers,
Loyal
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Old 08-02-2012, 08:37 AM   #29
vyellapa
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Hi Loyal,
I tried reloading the database and got the same error. If it has anything to do with versioning, I am using R 2.15.1 and cufflinks 2.0.0 with Cummerbund 1.99.

Is there any other way I could try?

Code:
> cuff<-readCufflinks()
> myGenes <- getGenes(cuff, myGeneIds)
Getting gene information:
	FPKM
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)
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Old 08-03-2012, 11:59 AM   #30
IBseq
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HI everyone,
have you ever had something like this when running cummerbund?

> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object(s) are masked from ‘package:stats’:

hclust

> cuff <- readCufflinks(dir=system.file("myextdata", package="cummeRbund"))
> cuff
CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS

it's all empty!
my cuffdiff outputs come from galaxy, they are in tabular format..

cheers
ib
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Old 08-08-2012, 04:43 PM   #31
lgoff
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Quote:
Originally Posted by vyellapa View Post
Hi Loyal,
I tried reloading the database and got the same error. If it has anything to do with versioning, I am using R 2.15.1 and cufflinks 2.0.0 with Cummerbund 1.99.

Is there any other way I could try?

Code:
> cuff<-readCufflinks()
> myGenes <- getGenes(cuff, myGeneIds)
Getting gene information:
	FPKM
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)
I'm curious as to where the ")" is coming from. Is this somewhere in your 'myGenes'?

-Loyal
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Old 08-14-2012, 05:16 AM   #32
Alex.Manuel
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Wink

Hi Loyal,
I'm a newbie in RNAseq and bioinformatics as well. So for me it is a hard way to get into all the "voodoo" .
Currently I have the same issue like vyellapa. I also use the newest software versions...

> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)
> diffGenes<-getGenes (cuff,diffGeneIDs)
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)


cheers
Alex
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Old 10-08-2012, 09:19 AM   #33
tankman
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Default RS-DBI driver errors in cummerbund 2.0

Hi Loyal,

Same type of issue (I'm getting driver errors), not sure what to do!

thanks!

tm

> cuff
CuffSet instance with:
3 samples
81928 genes
276141 isoforms
167337 TSS
0 CDS
245784 promoters
502011 splicing
0 relCDS
> gene.repFpkm<-repFpkm(genes(cuff))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
>
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] cummeRbund_2.0.0 Gviz_1.2.0 rtracklayer_1.18.0 GenomicRanges_1.10.1 IRanges_1.16.2
[6] fastcluster_1.1.7 reshape2_1.2.1 ggplot2_0.9.2.1 RSQLite_0.11.2 DBI_0.2-5
[11] BiocGenerics_0.4.0 BiocInstaller_1.8.1

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.0 Biobase_2.18.0 biomaRt_2.14.0 Biostrings_2.26.1 biovizBase_1.6.0
[6] bitops_1.0-4.1 BSgenome_1.26.0 cluster_1.14.2 colorspace_1.1-1 dichromat_1.2-4
[11] digest_0.5.2 GenomicFeatures_1.10.0 gtable_0.1.1 Hmisc_3.9-3 labeling_0.1
[16] lattice_0.20-10 MASS_7.3-22 memoise_0.1 munsell_0.4 parallel_2.15.1
[21] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.95-0.1.2 Rsamtools_1.10.1
[26] scales_0.2.2 stats4_2.15.1 stringr_0.6.1 tools_2.15.1 XML_3.95-0.1
[31] zlibbioc_1.4.0
>

Quote:
Originally Posted by lgoff View Post
I'm curious as to where the ")" is coming from. Is this somewhere in your 'myGenes'?

-Loyal
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Old 10-08-2012, 09:24 AM   #34
lgoff
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tankman,
Can you send me your cuffData.db file? I will try to see if I can pinpoint the problem.

Thanks

-Loyal
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Old 10-08-2012, 09:28 AM   #35
tankman
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Hello Loyal,

It's a bit big --~ 5 Gb.

can you create a dummy account for me and i can scp it over?
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Old 10-31-2012, 09:52 AM   #36
bparr
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Hi,

I am having trouble with the 'features' method in version 2.0.0. Going through the manual everything seems to behave nicely, except I keep hitting errors when I try to look at gene feature plots. This appears to be a result of a null data frame being returned from the features() method when called on a CuffGene instance. Has anyone else run into this before, or have any recommendations on what to do differently (relative to the online manual)? I did create the cuffData database with the genome build and transcript gtf set.

>
> myGene
CuffGene instance for gene XLOC_000301
Short name: PINK1
Slots:
annotation
features
fpkm
repFpkm
diff
count
isoforms CuffFeature instance of size 5
TSS CuffFeature instance of size 3
CDS CuffFeature instance of size 1
> features(myGene)
[1] seqnames start end width
[5] strand source type score
[9] phase exon_number gene_biotype gene_id
[13] gene_name protein_id isoform_id transcript_name
<0 rows> (or 0-length row.names)
>

Thanks,
bparr
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Old 01-17-2013, 04:13 AM   #37
Frithjof
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Hi,

I can confirm the problem of bparr above. Seems the CuffGene features are not created/interpreted correctly.
Subsequently the gene feature plots are giving an error, when calling the function "makeGeneRegionTrack"

Any ideas how to fix this ?

Thanks
Frithjof



> cuff
CuffSet instance with:
2 samples
119511 genes
406612 isoforms
201547 TSS
77479 CDS
119511 promoters
201547 splicing
18611 relCDS

> myGene
CuffGene instance for gene XLOC_000020
Short name: RP11-206L10.6,RP11-206L10.7,RP11-206L10.9
Slots:
annotation
features
fpkm
repFpkm
diff
count
isoforms CuffFeature instance of size 8
TSS CuffFeature instance of size 6
CDS CuffFeature instance of size 0

head(fpkm(myGene))
gene_id sample_name fpkm conf_hi conf_lo quant_status
1 XLOC_000020 cond1 0.747664 3.16391 0 OK
2 XLOC_000020 cond2 0.380987 1.71967 0 OK

> head(features(myGene))
[1] feature_id gene_id isoform_id seqnames source type start end
[9] score strand frame
<0 rows> (or 0-length row.names)

> genetrack<-makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) :
undefined columns selected



> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 GenomicRanges_1.10.5
[5] IRanges_1.16.4 fastcluster_1.1.7 reshape2_1.2.2 ggplot2_0.9.3
[9] RSQLite_0.11.2 DBI_0.2-5 BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0
[4] Biostrings_2.26.2 biovizBase_1.6.2 bitops_1.0-5
[7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-0
[10] dichromat_1.2-4 digest_0.6.0 GenomicFeatures_1.10.1
[13] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1
[16] lattice_0.20-13 MASS_7.3-23 munsell_0.4
[19] parallel_2.15.2 plyr_1.8 proto_0.3-10
[22] RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2
[25] scales_0.2.3 stats4_2.15.2 stringr_0.6.2
[28] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0
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Old 01-17-2013, 06:01 AM   #38
lgoff
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Hi guys,
Please make sure that when you are building your cuffData.db file (with readCufflinks()) that you are providing values to both the 'gtfFile' and 'genome' arguments. Also, the .gtf file MUST be the same .gtf file that you used for cuffdiff as this will guarantee that the gene_id and other feature IDs will map appropriately.

cuff<-readCufflinks(gtfFile='myTranscriptome.gtf',genome='mm9')

If you did not do this from the get-go, you can do the following:

cuff<-readCufflinks(gtfFile='myTranscriptome.gtf',genome='mm9',rebuild=T)

to rebuild the database and add these elements to the cuffData.db database. These are not populated by default when you run readCufflinks. I make this a bit more seamless in later versions of cummeRbund.

Cheers,
Loyal
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Old 01-17-2013, 07:02 AM   #39
Frithjof
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Dear Loyal,

thank you for the quick response. Indeed I used the merged.gtf file from cuffmerge for the initial DB construction. Using the gtf from the cufflinks input yet produces a new error also resulting from an empty features set.

Obviously the features are not imported properly. Any suggestions where this might originate from and how to fix this ?

Thanks
Frithjof

>cuff<-readCufflinks(gtfFile="./Homo_sapiens.GRCh37.68.clean.gtf",
genome="hg19",rebuild=T)

> myGene
CuffGene instance for gene XLOC_000020
Short name: RP11-206L10.6,RP11-206L10.7,RP11-206L10.9
Slots:
annotation
features
fpkm
repFpkm
diff
count
isoforms CuffFeature instance of size 8
TSS CuffFeature instance of size 6
CDS CuffFeature instance of size 0

> head(features(myGene))
[1] seqnames start end width strand
[6] source type score phase gene_id
[11] isoform_id exon_number gene_name gene_biotype transcript_name
[16] protein_id
<0 rows> (or 0-length row.names)

> genetrack<-makeGeneRegionTrack(myGene)
Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "IRanges") :
Rle of type 'list' is not supported
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Old 01-17-2013, 07:06 AM   #40
lgoff
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Can you post the lines of the .gtf file that correspond to the gene_id 'XLOC_000020'

grep "XLOC_000020" ./Homo_sapiens.GRCh37.68.clean.gtf

I'd like to see what the structure of your .gtf file looks like. If there I can't find anything in this, perhaps you can send me your .gtf file and cuffData.db so I can take a peek and see what happened in the import.

Thanks,
Loyal
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