Hi Joern,

thanks I will try that. I am sorry for not sending to the list, was not on
purpose.
With kind regards,
Andreia

On Fri, Jun 25, 2010 at 2:02 PM, Joern Toedling <Joern.Toedling@curie.fr>wrote:

> Hi Andreia,
>
> please keep the discussion on the list, in order to have the answers stored
> in
> the mailing list archives.
> For reading in GFF (version 3) files, I am using the function "readGff3"
> from
> package genomeIntervals. However, if you look at the code of that function
> (simply type in 'readGff3' without brackets), you see that the process is
> straightforward. The file is first read into R (using funcion 'scan') and
> then
> a "Genome_intervals_stranded" object is constructed from the result. Since
> the
> format GTF is very similar to GFF, you can likely use the same source code
> line-by-line with only minor changes. For example, in the attributes field,
> I
> think that GFF requires a "=" between attribute and value and GTF a
> whitespace. So after reading in the file with "scan", you might want to
> replace those whitespaces at those positions by equal signs, using for
> example
> the function 'gsub'.
>
> HTH,
> Joern
>
>
> On Fri, 25 Jun 2010 13:16:55 +0100, Andreia Fonseca wrote
> > Dear Joern,
> >
> > Thank you for your quick reply. Now its working well!!!! I have one more
> question. Concerning the annotation file, I have a gtf file with all the
> annotation of the human genome. I saw in your annotation script that you
> show
> how to read gff files. Can you give me a hint on how to read the gtf file.
> > Thanks
> > with kind regards,
> > Andreia
> >
> > On Thu, Jun 24, 2010 at 4:26 PM, Joern Toedling <Joern.Toedling@curie.fr
> >
> wrote:
> >  Hi Andreia,
> >
> > when "reducing" overlapping aligned reads, also the consensus sequence of
> the
> > merged reads is determined, using the function consensusString from
> package
> > Biostrings. And for some reason this step does not work for you.
> >
> > I cannot be completely sure but I think there may be an issue with the
> way
> > that you generate the AlignedGenomeIntervals object. The recommended way
> is
> > to use package ShortRead first to generate an AlignedRead object and then
> > coercing that object into an AlignedGenomeIntervals object. However,
> creating
> > it manually is possible but more prone to such problems.
> > However, thank you very much for trying it and reporting the results,
> maybe I
> > need to implement an additional check of the object to provide users in
> this
> > case with a more meaningful error message.
> >
> > I think the problem here is that your specified read sequence always
> seems to
> > be one shorter than the specified interval lengths.
> > For example, in the first row the sequence
> > TTTCTAATGAGCCCAGGGAGGGCTAGA
> > has 27 letters but the interval goes from position 43076512 to 43076539,
> which
> > is 28 bases. So maybe your alignment coordinates are in half-open
> interval
> > notation, in which case the interval actually ends at position 43076538.
> Then
> > the argument 'end' should be:
> > end=data$V6-1L
> > Also note that the coordinates in girafe are 1-based, so you may need to
> > adjust the alignment coordinates accordingly.
> >
> > It could also be an issue with factors in your data.frame 'data' (which
> btw.
> > is not a very good name since there also is a basic R function of that
> name),
> > especially the strand could be a candidate here. When you read in data
> using
> > read.table it's generally a good idea to use the argument
> > stringsAsFactors=FALSE to make sure there are no factor-related
> > errors later on unless you specifically want to make use of factors in
> your
> > data.frame.
> >
> > Please let me know if these suggested changes resolve the problem.
> Otherwise,
> > I would be grateful if you can send me a small excerpt of the file that
> you
> > read in with read.table off-list and I can have a closer look at it.
> >
> > Cheers,
> > Joern
>
>


-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral@fm.ul.pt
         andreia.fonseca@gmail.com

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