Thank you very much to the list and specially to all those who answered my
question.

I'm a little overwhelmed with all this tsumani of information right now,
but I expect to be able to use it in a short time.
I will test those solutions you offered me and try to determine which is
the best for me and come back to this post to comment about my strategy of
choice.
Thank you very very much, it's always a pleasure to be in contact with the
people in this list.

Best regards

JL


2014-06-23 9:47 GMT+02:00 Jose Garcia <garciamanteiga.josemanuel@hsr.it>:

> Hi Jose,
> All the options you have already had from the list work fine. My personal
> favourite one is to use htseq-count and then DESeq2 in R/Bioconductor. It
> has a specific function that takes the separate gene-counts table per
> sample and constructs an experiment-object for you with all the data you
> need for differential expression.
> Alternatively, if you have a very complicated design it could be
> convenient to use limma with the voom function for RNA-Seq data.
> Jose
>
>
>
> 2014-06-23 8:49 GMT+02:00 Hans-Rudolf Hotz <hrh@fmi.ch>:
>
>
>>
>> On 06/20/2014 02:27 PM, José Luis Lavín wrote:
>> > First of all I want to thank Michael for his swift answer.
>> >
>> > Then I have a concern about this, Am I wrong or the package
>> "easyRNASeq" is
>> > dramatically lacking an update at its bioconductor page. I mean that
>> manual
>> > script and vignette are not up to date (at least R complains when I try
>> to
>> > use functions such as "easyRNASeq" described on them).
>> >
>> > Any other alternatives that can be used for the table of count
>> generation
>> > task ?
>> >
>>
>> Have a look at the QuasR
>>
>> http://www.bioconductor.org/packages/release/bioc/html/QuasR.html
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>> > 2014-06-20 12:30 GMT+02:00 Michael Dondrup <michael.dondrup@ii.uib.no>:
>> >
>> >> Dear JosÃ©,
>> >>
>> >> easyRNAseq can do that.
>> >>
>> >> http://www.bioconductor.org/packages/release/bioc/html/easyRNASeq.html
>> >>
>> >> Best
>> >> Michael
>> >>
>> >> On Jun 20, 2014, at 11:56 AM, JosÃ© Luis LavÃ­n wrote:
>> >>
>> >>> Dear list members,
>> >>>
>> >>> I have to analyze bacterial transcriptomic data and I have a doubt
>> about
>> >>> how to proceed.
>> >>>
>> >>> I have downloaded the reference genome FASTA from the NCBI and also a
>> gff
>> >>> file containing the annotation of that reference. I can map the reads
>> to
>> >>> the genome and so on, but when the time comes to generate the table of
>> >>> counts for the Differential Expression (DE) analysis, I have no clear
>> >> Idea
>> >>> on how to use the gff annotation file to assign reads to the genomic
>> >>> features.
>> >>>
>> >>> I've looked for solutions like HTSeq, but to my understanding this
>> >> program
>> >>> will generate a table of counts per alignment file (for instance, one
>> >> table
>> >>> per each bam file) which will require to merge all the independent
>> tables
>> >>> one by one to generate the full table of count for the DE analysis...
>> >>>
>> >>> To sum up; Is there any R package that enable to generate a single
>> Table
>> >> of
>> >>> counts from multiple BAM files using an annotation gff file (or
>> similar),
>> >>> for a genome that is not included in the UCSC catalog of reference
>> >>> organisms (as is the case of this bacteria I have to analyze)?
>> >>>
>> >>> Thanks in advance
>> >>>
>> >>> JL
>> >>>
>> >>> PD. I came across "Rsubread" package, but...
>> >>>
>> >>> package â€˜Rsubreadâ€™ is not available (for R version 3.1.0)
>> >>>
>> >>>> sessionInfo()R version 3.1.0 (2014-04-10)
>> >>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> >>>
>> >>> locale:
>> >>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> >>> Kingdom.1252
>> >>> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
>> >>> [5] LC_TIME=English_United Kingdom.1252
>> >>>
>> >>> attached base packages:
>> >>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> >>>
>> >>> other attached packages:
>> >>> [1] BiocInstaller_1.14.2
>> >>>
>> >>> loaded via a namespace (and not attached):
>> >>> [1] tools_3.1.0
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> --
>> >>> JosÃ© Luis LavÃ­n Trueba, Ph.D
>> >>>
>> >>> Genome Analysis Platform
>> >>> CIC bioGUNE
>> >>> Parque TecnolÃ³gico de Bizkaia
>> >>> Building 502, Floor 0
>> >>> 48160 Derio-Spain
>> >>>
>> >>> Tel.: +34 946 572 524
>> >>> Fax: +34 946 568 732
>> >>>
>> >>>        [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
>> >>> Bioconductor mailing list
>> >>> Bioconductor@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@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@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> Jose M. Garcia Manteiga PhD
> Data Analysis in Functional Genomics
> Center for Translational Genomics and BioInformatics
> Dibit2-Basilica, 4A3
> San Raffaele Scientific Institute
> Via Olgettina 58, 20132 Milano (MI), Italy
>
> Tel: +39-02-2643-9144
> e-mail: garciamanteiga.josemanuel@hsr.it
>



-- 
-- 
José Luis Lavín Trueba, Ph.D

Genome Analysis Platform
CIC bioGUNE
Parque Tecnológico de Bizkaia
Building 502, Floor 0
48160 Derio-Spain

Tel.: +34 946 572 524
Fax: +34 946 568 732

	[[alternative HTML version deleted]]

