Yes, indeed, I would like to mine into the fascicularis transcriptome and using makeTranscriptDbFromGFF() with my gff file is a very good suggestion. I tried earlier this approach but I have to confess that I was unable to specify an exonRankAttributeName value. I shall try to figure it out more carefully later. Thank you Ugo Le 16-07-2014 10:58, Marc Carlson a ?crit?: > Yes you definitely can use makeTranscriptDbFromGFF if you want a > TranscriptDb object. The following works for example: > > library("GenomicFeatures") > txdb <- makeTranscriptDbFromGFF( > file="ref_Macaca_fascicularis_5.0_top_level.gff3.gz", > format="gff3", > exonRankAttributeName=NA, > gffGeneIdAttributeName=NA, > chrominfo=NA, > dataSource=NA, > species=NA, > circ_seqs=DEFAULT_CIRC_SEQS, > miRBaseBuild=NA, > useGenesAsTranscripts=FALSE) > > But is massaging this into a transcriptome what we want here? Ugo > hasn't told us what he wants to do with this data. Also I didn't look > closely at the data itself. It may be that you can specify a value > for exonRankAttributeName (which is always what you should want to do > if you can manage it). > > > Marc > > > > On 07/16/2014 09:10 AM, Michael Lawrence wrote: >> Is there anything makeTranscriptDbFromGFF could do to help with this? >> Sounds like you typically want something like a TxDb, except perhaps >> with >> some special considerations. Following the NCBI conventions is >> probably >> worth it. >> >> >> On Wed, Jul 16, 2014 at 8:58 AM, Chris Stubben <stubben at="" lanl.gov=""> >> wrote: >> >>> I would also suggest using rtracklayer import or create a genome data >>> package. At least for microbial genomes, you often just need to >>> return >>> features (CDS, pseudogenes, tRNAs, etc) that have a parent with a >>> locus_tag >>> key and assign that locus tag to the child (the read.gff default), so >>> that's what is getting messed up with your large file. >>> I'll probably use the rtracklayer import object in future versions >>> instead >>> and then join on Parent where locus_tag is NA to the ID where >>> locus_tag is >>> not NA. >>> Chris >>> >>> >>> >>> I cc'd the packageMaintainer(), so that they are more likely to see >>> this >>>> post. >>>> >>> I don't know whether this helps in this particular case, but >>> packages >>>> should be using rtracklayer::import rather than creating their own >>>> readers. >>>> Then at least whatever deficiencies are identified and corrected >>>> benefit >>>> the entire project. >>>> >>> >>> >>> >>> -- >>> >>> Chris Stubben >>> >>> Los Alamos National Lab >>> Bioscience Division >>> MS M888 >>> Los Alamos, NM 87545 >>> >>> Phone: (505) 667-3295 >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor