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Question: regarding makeTranscriptDbFromGFF
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5.1 years ago by
deepika lakhwani170 wrote:
Hello I apologize for bothering you again. I wanted to use makeTranscriptDbFromGFF function but after loading the Genomicfeatures package and run makeTranscriptDbFromGFF(). I got error Error: could not find function "makeTranscriptDbFromGFF" I do not know that What am I doing wrong. I ran: > txdb <-makeTranscriptDbFromGFF(file = 'mm9.gtf', format = "gtf",exonRankAttributeName = "exon_number", chrominfo = chrominfo, dataSource = "UCSC", species = "Mus musculus") Error: could not find function "makeTranscriptDbFromGFF" then i ran makeTranscriptDbFromGFF() Error: could not find function "makeTranscriptDbFromGFF" please resolve my problem. thanking you regards deepika [[alternative HTML version deleted]]
modified 5.1 years ago by James W. MacDonald48k • written 5.1 years ago by deepika lakhwani170
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5.1 years ago by
United States
James W. MacDonald48k wrote:
Hello I am creating transcriptDb object from GFF file using maketranscriptDbFromGFF. I have sequencing data and mapped this data on rice genome using tophat now i want to count the overlaps of my genomic alignments with genes but when i ran it : txdb <- makeTranscriptDbFromGFF(file = "all.gff3",format="gff",dataSource=" ftp://ftp.plantbiology.msu.edu",exonRankAttributeName="exon_number",sp ecies="oryza sativa") Error in DataFrame(...) : different row counts implied by arguments and when i remove dataSource then again got the same error. txdb <- makeTranscriptDbFromGFF(file = "all.gff3", format= "gff",exonRankAttributeName= "exon_number",chrominfo = "chrominfo",species="oryza sativa") Error in DataFrame(...) : different row counts implied by arguments Finally i remove dataSource, chromoinfo but again failed. txdb <- makeTranscriptDbFromGFF(file = "all.gff3",format="gff",species="oryza sativa") extracting transcript information Extracting gene IDs extracting transcript information Processing splicing information for gff3 file. Deducing exon rank from relative coordinates provided Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo from available sequence names. No chromosome length information is available. Warning messages: 1: In .deduceExonRankings(exs, format = "gff") : Infering Exon Rankings. If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName 2: In matchCircularity(chroms, circ_seqs) : None of the strings in your circ_seqs argument match your seqnames. actually i am trying so many times but everytime i got error. please tell me how to solve this problem. sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 LC_MONETARY=English_India.1252 [4] LC_NUMERIC=C LC_TIME=English_India.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.12.4 AnnotationDbi_1.22.6 Biobase_2.20.1 GenomicRanges_1.12.5 IRanges_1.18.4 [6] BiocGenerics_0.6.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 DBI_0.2-7 RCurl_1.95-4.1 [7] Rsamtools_1.12.4 RSQLite_0.11.4 rtracklayer_1.20.4 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 [13] zlibbioc_1.6.0 regards Deepika [[alternative HTML version deleted]]
Hi, If your last attempt didn't work (I'll keep that portion of your email quoted below) there should be an error that was reported, but I only see warnings. Are there errors that come up after this? > Finally i remove dataSource, chromoinfo but again failed. > > txdb <- makeTranscriptDbFromGFF(file = > "all.gff3",format="gff",species="oryza sativa") > extracting transcript information > Extracting gene IDs > extracting transcript information > Processing splicing information for gff3 file. > Deducing exon rank from relative coordinates provided > Prepare the 'metadata' data frame ... metadata: OK > Now generating chrominfo from available sequence names. No chromosome > length information is available. > Warning messages: > 1: In .deduceExonRankings(exs, format = "gff") : > Infering Exon Rankings. If this is not what you expected, then please be > sure that you have provided a valid attribute for exonRankAttributeName > 2: In matchCircularity(chroms, circ_seqs) : > None of the strings in your circ_seqs argument match your seqnames. Is there something more that is outputted that's missing from your email? The fact that there are no errors reported suggests that you should now have a functional(?) txdb object ... do you? -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
Hii... Ok, i got it. Actually i was thinking warning message also an error and yes its a fuctional txdb and trying so many fuctions and it works.If i want to add chromosome information then what should i do. I am trying but it did not work. I am learning these new things so apologize for asking very basic question. Thanks for your response. On Thu, Sep 26, 2013 at 6:59 PM, Steve Lianoglou <lianoglou.steve@gene.com>wrote: > Hi, > > If your last attempt didn't work (I'll keep that portion of your email > quoted below) there should be an error that was reported, but I only > see warnings. > > Are there errors that come up after this? > > > Finally i remove dataSource, chromoinfo but again failed. > > > > txdb <- makeTranscriptDbFromGFF(file = > > "all.gff3",format="gff",species="oryza sativa") > > extracting transcript information > > Extracting gene IDs > > extracting transcript information > > Processing splicing information for gff3 file. > > Deducing exon rank from relative coordinates provided > > Prepare the 'metadata' data frame ... metadata: OK > > Now generating chrominfo from available sequence names. No chromosome > > length information is available. > > Warning messages: > > 1: In .deduceExonRankings(exs, format = "gff") : > > Infering Exon Rankings. If this is not what you expected, then please > be > > sure that you have provided a valid attribute for exonRankAttributeName > > 2: In matchCircularity(chroms, circ_seqs) : > > None of the strings in your circ_seqs argument match your seqnames. > > Is there something more that is outputted that's missing from your > email? The fact that there are no errors reported suggests that you > should now have a functional(?) txdb object ... do you? > > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > [[alternative HTML version deleted]]