Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    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

    Comment


    • #32
      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

      Comment


      • #33
        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
        >

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

        -Loyal

        Comment


        • #34
          tankman,
          Can you send me your cuffData.db file? I will try to see if I can pinpoint the problem.

          Thanks

          -Loyal

          Comment


          • #35
            Hello Loyal,

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

            can you create a dummy account for me and i can scp it over?

            Comment


            • #36
              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

              Comment


              • #37
                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

                Comment


                • #38
                  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

                  Comment


                  • #39
                    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

                    Comment


                    • #40
                      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

                      Comment


                      • #41
                        Ok, problem solved ...
                        As mentioned above I first tried the merged.gtf from cuffmerge and also the original .gtf provided to cufflinks. Both giving me errors.
                        I now re-run the analysis, deleting the old .db first and then recreating the DB with the merged.gtf file from cuffmerge.

                        Now everything seems to work fine.

                        Thank you again Loyal for the immediate help

                        Cheers
                        Frithjof

                        Comment


                        • #42
                          Hi Loyal,

                          I have the same problem when ran makeGeneRegionTrack().
                          I've done with previously solutions but it doesn't seem to work for me.
                          I am also confused the genome argument. Should I have to tell makeGeneRegionTrack() the exactly name indicating which genome builds to the .gtf annotation?

                          What information I have are shown below:
                          diff_out: is a output directory from cuffdiff
                          merged.gtf: is a gtf file from cuffmerge (I post in the bottom and it has a gene_id in the merged.gtf)

                          Code:
                          cuff<-readCufflinks('diff_out',gtfFile='diff_out/merged.gtf',rebuild=T,genome='tb427')
                          Code:
                          > myGene
                          CuffGene instance for gene XLOC_000166 
                          Short name:	 Tb427.01.710 
                          Slots:
                          	 annotation
                          	 features
                          	 fpkm
                          	 repFpkm
                          	 diff
                          	 count
                          	 isoforms	 CuffFeature instance of size 1 
                          	 TSS		 CuffFeature instance of size 1 
                          	 CDS		 CuffFeature instance of size 1
                          Code:
                          > head(features(myGene))
                           [1] seqnames   start      end        width      strand     source    
                           [7] type       score      phase      isoform_id gene_id    gene_name 
                          <0 rows> (or 0-length row.names)
                          Code:
                          > genetack<-makeGeneRegionTrack(myGene)
                          Error in `[.data.frame`(features(object), , featCols) : 
                            undefined columns selected
                          Code:
                          Tb427_01_v4 Cufflinks exon  228118  229962  . - . gene_id "XLOC_000165"; transcript_id "TCONS_00000307"; exon_number "1"; gene_name "Tb427.01.670"; oId "rna_Tb427.01.670-1"; contained_in "TCONS_00000296"; nearest_ref "rna_Tb427.01.670-1"; class_code "="; tss_id "TSS296"; p_id "P256";
                          Tb427_01_v4 Cufflinks exon  230768  231499  . - . gene_id "XLOC_000165"; transcript_id "TCONS_00000308"; exon_number "1"; gene_name "Tb427.01.690"; oId "rna_Tb427.01.690-1"; contained_in "TCONS_00000296"; nearest_ref "rna_Tb427.01.690-1"; class_code "="; tss_id "TSS297"; p_id "P257";
                          Tb427_01_v4 Cufflinks exon  232575  233897  . - . gene_id "XLOC_000165"; transcript_id "TCONS_00000309"; exon_number "1"; gene_name "Tb427.01.700"; oId "rna_Tb427.01.700-1"; contained_in "TCONS_00000296"; nearest_ref "rna_Tb427.01.700-1"; class_code "="; tss_id "TSS285"; p_id "P258";
                          Tb427_01_v4 Cufflinks exon  234247  235509  . - . gene_id "XLOC_000166"; transcript_id "TCONS_00000310"; exon_number "1"; gene_name "Tb427.01.710"; oId "rna_Tb427.01.710-1"; nearest_ref "rna_Tb427.01.710-1"; class_code "="; tss_id "TSS298"; p_id "P260";
                          Tb427_01_v4 Cufflinks exon  235715  237370  . - . gene_id "XLOC_000167"; transcript_id "TCONS_00000311"; exon_number "1"; gene_name "Tb427.01.720"; oId "rna_Tb427.01.720-1"; nearest_ref "rna_Tb427.01.720-1"; class_code "="; tss_id "TSS299"; p_id "P261";
                          Tb427_01_v4 Cufflinks exon  240449  241756  . - . gene_id "XLOC_000169"; transcript_id "TCONS_00000313"; exon_number "1"; gene_name "Tb427.01.740"; oId "rna_Tb427.01.740-1"; nearest_ref "rna_Tb427.01.740-1"; class_code "="; tss_id "TSS301"; p_id "P263";
                          Many thanks in advance.

                          Comment


                          • #43
                            I have the same problem!


                            > sig_gene_unic<-getGenes(cuff,gene_uniq)
                            Erreur dans sqliteExecStatement(conn, statement, ...) :
                            RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

                            Help please

                            Comment


                            • #44
                              getGenes error

                              Hi,

                              I am getting an error when I create gene sets with the last version of cufflinks (2.0.2).When I rebuild the cuffData.db (rebuild=T) as suggested by Loyal, I always get the error «*RS-DBI driver: (error in statement: near ")": syntax error)*»

                              Any help much appreciated, commands below,
                              Steph

                              > cuff_data <- readCufflinks('Diff_out',rebuild=T)
                              > cuff_data
                              CuffSet instance with: 3 samples
                              43025 genes
                              43025 isoforms
                              0 TSS
                              0 CDS
                              0 promoters
                              0 splicing
                              0 relCDS
                              > data(sampleData)
                              > myGeneIds<-sampleIDs
                              > myGeneIds
                              [1] "XLOC_001363" "XLOC_001297" "XLOC_001339" "XLOC_000132" "XLOC_001265"
                              [6] "XLOC_000151" "XLOC_001359" "XLOC_000069" "XLOC_000170" "XLOC_000105"
                              [11] "XLOC_001262" "XLOC_001348" "XLOC_001411" "XLOC_001369" "XLOC_000158"
                              [16] "XLOC_001370" "XLOC_001263" "XLOC_000115" "XLOC_000089" "XLOC_001240"

                              > myGenes<-getGenes(cuff_data,myGeneIds)
                              Getting gene information:
                              FPKM
                              Erreur dans sqliteExecStatement(con, statement, bind.data) :
                              RS-DBI driver: (error in statement: near ")": syntax error)


                              > sessionInfo()
                              R version 2.15.3 (2013-03-01)
                              Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

                              other attached packages:
                              [1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2
                              [4] GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.9
                              [7] reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.2
                              [10] DBI_0.2-5 BiocGenerics_0.4.0

                              loaded via a namespace (and not attached):
                              [1] AnnotationDbi_1.20.7 Biobase_2.18.0 biomaRt_2.14.0
                              [4] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5
                              [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1
                              [10] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.10.2
                              [13] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1
                              [16] lattice_0.20-14 MASS_7.3-23 munsell_0.4
                              [19] parallel_2.15.3 plyr_1.8 proto_0.3-10
                              [22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.10.2
                              [25] scales_0.2.3 stats4_2.15.3 stringr_0.6.2
                              [28] tools_2.15.3 XML_3.96-0.2 zlibbioc_1.4.0

                              Comment


                              • #45
                                Dear All
                                I got problem with cummeRbund.... my RNA-seq data has fusion gene HLA-DQB1. When I conducted diff analysis (cufflinks), cummeRbund can not show this gene. I tried HLA-DQB1, HLADQB1, HLADQB, HLA, DQB1, DQB etc... it says:
                                > mygene<- getGene(cuff_data,'HLA-DQB1')
                                No gene set returned (Gene might not be in database?)
                                Error in validObject(.Object) : invalid class “CuffGene” object: FALS

                                However, I can find other genes with no problem with same commands...

                                Is anybody out there has somthing to help me ?
                                Thanks in advance.

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Techniques and Challenges in Conservation Genomics
                                  by seqadmin



                                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                  Avian Conservation
                                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                  03-08-2024, 10:41 AM
                                • seqadmin
                                  The Impact of AI in Genomic Medicine
                                  by seqadmin



                                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                                  02-26-2024, 02:07 PM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 03-14-2024, 06:13 AM
                                0 responses
                                34 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-08-2024, 08:03 AM
                                0 responses
                                72 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-07-2024, 08:13 AM
                                0 responses
                                81 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-06-2024, 09:51 AM
                                0 responses
                                68 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X