Originally posted by vyellapa
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> 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)
cuff<-readCufflinks('diff_out',gtfFile='diff_out/merged.gtf',rebuild=T,genome='tb427')
> 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
> 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)
> genetack<-makeGeneRegionTrack(myGene) Error in `[.data.frame`(features(object), , featCols) : undefined columns selected
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";
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