hey I just remembered why you (Wei) put my name on the package in the first
place ;-)

require(Rsubread)
?createAnnotationFile

require(TxDb.Hsapiens.UCSC.hg18.knownGene)
createAnnotationFile(transcripts(TxDb.Hsapiens.UCSC.hg18.knownGene))
##
## Your GRanges elementMetadata must contain a column called "id".
## Error in
createAnnotationFile(transcripts(TxDb.Hsapiens.UCSC.hg18.knownGene)) :
##  Aborting.
##
## ...oops, looks like I need to write another patch in order for this to
"do what you mean"...
## ...meanwhile

txs <- transcripts(TxDb.Hsapiens.UCSC.hg18.knownGene)
txs$id <- txs$tx_id ## doh
createAnnotationFile(txs, fname='transcripts.hg18.txt')
## Annotations were sucessfully written to transcripts.hg18.txt

Alright this could be a little smoother, that said, both the "generate an
index from a BSgenome" and "generate new annotations from a TxDb, ideally
as an installable package" requests are sensible.

Me personally, my biggest request is to make QuasR work with subread, so
that I can do idiotic things like realign bisulfite-converted genomes on my
laptop.  Not because it's a good idea, but because I can :-)





On Tue, Jul 2, 2013 at 3:27 AM, Wei Shi <shi@wehi.edu.au> wrote:

> Dear Diego,
>
> You can provide your own annotation to featureCounts via the 'annot'
> parameter. Have a look at the help page of featureCounts, which describes
> the formats of external annotations allowed by featureCounts. I imagine it
> wouldn't be too hard to generate a data frame from a bioc annotation and
> then feed it to featureCounts.
>
> Best wishes,
>
> Wei
>
>
>
> On Jul 2, 2013, at 12:31 PM, Diego Diez wrote:
>
> > Dear Wei
> >
> > I recently gave a try to Rsubread/featureCounts() but found that
> featureCounts only supports mm9, mm10 and hg19 assemblies (using the
> XXX_RefSeq_exon.txt files with XXX being one of the assemblies mentioned).
> Would it be possible to modify this function to obtain this information
> from Bioconductor annotation packages? That would allow anyone to use mm8,
> hg18 or use featureCounts() with other species if needed and the
> corresponding data is present. A similar interface to generate the index
> files from the genome sequences (from the Bioconductor genome annotation
> packages) for the alignment step would be extremely useful.
> >
> > Best wishes,
> > Diego
> >
> >
> > On Tue, Jul 2, 2013 at 9:02 AM, Wei Shi <shi@wehi.edu.au> wrote:
> > Dear All,
> >
> > I would like to formally introduce to you the featureCounts function
> included in the Rsubread package. featureCounts is R function designed for
> summarizing sequencing reads to genomic features such as genes, exons and
> promoters. It is a light-weight general-purpose read counting program
> (essentially written in C), and it has the following features:
> > (1) It performs precise read assignments by taking care of indels,
> junctions and fusions in the reads.
> > (2) It takes less than 4 minutes to summarize 20 million pairs of reads
> to 26k RefSeq genes using one thread, and only uses 40MB of memory (you can
> even run it on a Mac laptop).
> > (3) It supports multi-threaded running.
> > (4) It supports GTF format annotation and SAM/BAM read data.
> > (5) It supports strand-specific read summarization.
> > (6) It can perform read summarization at both feature level (eg. exons)
> and meta-feature level (eg. genes).
> > (7) It allows users to specify whether reads overlapping with more than
> one feature should be counted or not.
> > (8) It gives users full control on the summarization of paired-end
> reads, including allowing them to check if both ends are mapped and/or if
> the paired-end distances satisfy the distance criteria.
> > (9) It discriminates the features, which were overlapped by both ends
> from the same fragment, from those which were overlapped by only one end so
> as to get more fragments counted.
> > (10) It allows users to specify whether chimeric fragments should be
> counted.
> > (11) It can exclude multi-mapping reads and reads with low mapping
> quality scores from summarization.
> >
> > To use this function, make sure you are using the latest version of
> Rsubread (1.10.5 in the release branch).
> >
> > A technical report for featureCounts can be found here -
> http://arxiv.org/abs/1305.3347. You may also refer to the Rsubread users
> guide for some details about this function (typing 'RsubreadUsersGuide()'
> in your R session).
> >
> > To see how featureCounts can be used in an RNA-seq analysis pipeline,
> you may have a look at this case study -
> http://bioinf.wehi.edu.au/RNAseqCaseStudy . This case study will also be
> used in a Workshop in the incoming Bioc2013 meeting.
> >
> > Hope you find it useful.
> >
> > Best wishes,
> >
> > Wei
> >
> > ______________________________________________________________________
> > The information in this email is confidential and inte...{{dropped:20}}
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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