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Old 06-11-2014, 03:43 AM   #1
Parharn
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Default Annotation for S. pombe in GAGE.

I am trying this workflow: "RNA-Seq Data Pathway and Gene-set Analysis Workflows
Weijun Luo" but on S. pombe and not human data.
In part 3.2 it starts with:

> library(TxDb.Hsapiens.UCSC.hg19.knownGene)

I need help with finding the corresponding package for S. pombe!

Please help!
/Parham
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Old 06-11-2014, 10:37 AM   #2
bigmw
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You would need to construct your own TranscriptDb object using function like makeTranscriptDbFromGFF from the GenomicFeatures package:
library(GenomicFeatures)
?makeTranscriptDbFromGFF

You may download the GFF data for S. pombe genome from:
http://www.pombase.org/downloads/gen...asets#features
I haven’t go through the whole process, but it should work theoretically.

In addition, makeTranscriptDbFromUCSC and makeTranscriptDbFromBiomart in GenomicFeatures package are more staightfoward for species with genome annotation in UCSC or Biomart database. UCSC does not have annotation data for S. pombe genome. You may try makeTranscriptDbFromBiomart if you confirmed Biomart has the data.
More details on GenomicFeatures package:
http://www.bioconductor.org/packages...cFeatures.html
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Old 06-11-2014, 10:46 AM   #3
Parharn
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Thanks for the tips bigmw, I will give it a try and see how it will goes.

Cheers,
/P
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Old 06-11-2014, 10:33 PM   #4
malcook
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Default makeTranscriptDbFromBiomart for S. pombe

I just posted an approach to using Biomart at https://www.biostars.org/p/103251/

Here's the nub:

Code:
txdb<-makeTranscriptDbFromBiomart(
            ,biomart ="fungi_mart_22"
            ,dataset = "spombe_eg_gene"
            ,host="fungi.ensembl.org"
            )
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