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

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