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Question: Gviz and Leishmania genomes
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gravatar for florian.hahne@novartis.com
4.0 years ago by
Switzerland
Hi Amel, I am afraid the information you provide is not enough for me to make any concrete suggestions. Without seeing the file how can I tell what is wrong about it? First of all, import.gff is a function from the rtracklayer package, and not from Gviz. This being said, Gviz utilises the function internally for building AnnotationTrack objects directly from GFF files. You may want to check the package vignette for more details on how to do that. You should be able to provide the path to the GFF directly to the AnnotationTrack constructor. However, this will not solve your problem. The error message is fairly explicit. Are you sure there are no additional comment lines or the like in your file? Can you read it using read.table? Do all lines really consist of 9 fields? Florian From: Amel Ghouila <amel.ghouila@gmail.com<mailto:amel.ghouila@gmail.com>> Date: Monday, November 18, 2013 11:37 AM To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: Re: Gviz and Leishmania genomes Dear Florian, I am trying to read GFF files (downoladed from tritypDB) with the import.gff command... but something is not working. I chked my GFF file have 9 tab-separated columns. Could you please how should I do to to read a GFF into an AnnotationTrack object. Bellow you can find the command I used as well as the error message in yellow: test<- import.gff("./Documents/TriTrypDB-6.0_LmajorFriedlin.gff", version = "3",genome = "Leishmania major",asRangedData = FALSE) Erreur dans .local(con, format, text, ...) : GFF files must have 9 tab-separated columns I also used the options(ucscChromosomeNames = FALSE) command to let it accept other genome names. Thank you in advance for your help in this matter. Best regards, Amel Ghouila 2013/11/7 Amel Ghouila <amel.ghouila@gmail.com<mailto:amel.ghouila@gmail.com>> Thank you for your email. I going to read the whole Gviz Help document. Best regards, Amel Ghouila 2013/11/7 Hahne, Florian <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Hi Amel, you can use whatever genome you have. Obviously it will be harder to download gene models and the like for exotic genomes from places like UCSC and ENSEMBL, but you don't have to do this. There are many different options to get your annotations in. I would suggest you read through the package vignette which hopefully covers everything. Florian From: Amel Ghouila <amel.ghouila@gmail.com<mailto:amel.ghouila@gmail.com>> Date: Thursday, November 7, 2013 2:52 PM To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: Gviz and Leishmania genomes Dear Florian, I am trying to use Gviz for the visualisation of different Leishmania genomes and other parasitic genomes. Is it possible with Gviz? Or is it designed only for human genome? Should I download other specific packages? Is it possible to retrieve data (coordinates, etc.) from my own input files? Thank you in advance for your help Best regards, Amel Ghouila [[alternative HTML version deleted]]
ADD COMMENTlink written 4.0 years ago by florian.hahne@novartis.com1.5k
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