[BioC] Annotation files for bacterial genome RNAseq

[Hans-Rudolf Hotz]

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 at ii.uib.no>:
>
>> Dear José,
>>
>> easyRNAseq can do that.
>>
>> http://www.bioconductor.org/packages/release/bioc/html/easyRNASeq.html
>>
>> Best
>> Michael
>>
>> On Jun 20, 2014, at 11:56 AM, José Luis Lavín 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 ‘Rsubread’ 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
>>>
>>>
>>>
>>>
>>> --
>>> --
>>> 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]]
>>>
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>>
>>
>
>
>
>
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