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Old 09-11-2012, 02:09 AM   #1
glados
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Default DESeq - get chromosome

Hello all.

I've been searching for this question for hours now, and I give up and post it here instead. It should not be very complicated.

I have a long list of sig. genes in DESeq I would like to look at in more detail where the genes are located in the genome. How do I receive chromosome number (possibly location) for the genes in DESeq? I know how to get this information in Cuffdiff, but in DESeq I wonder if it's possible.
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Old 09-12-2012, 02:46 AM   #2
Simon Anders
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How have you made the count table that you used as input for DESeq? I suppose, by using a GTF file. And that one contains all the information you need.
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Old 09-12-2012, 02:55 AM   #3
glados
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Yes, by using a reference annotation gtf. How do you suggest I use it? If I have a long list with genes I want to look at. Perhaps I can compare them somehow. I'm new to bioinformatics so it's not intuitive to me yet.
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Old 09-12-2012, 09:49 AM   #4
dariober
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Quote:
Originally Posted by glados View Post
Yes, by using a reference annotation gtf. How do you suggest I use it? If I have a long list with genes I want to look at. Perhaps I can compare them somehow. I'm new to bioinformatics so it's not intuitive to me yet.
If you want to do it in R, this sample code will read the gtf file and extract the rows matching your list of genes:

Code:
## List (vector) of differentially expr. genes
degenes<- c('TNFRSF18', 'WASH7P') 

gtf<- read.table('genes.gtf', stringsAsFactors= FALSE, sep= '\t', quote= '')
gene_id<- sub('.*(gene_name \")', '', gtf$V9, perl= TRUE) ## NOTE: Replace gene_name with the feature to extract (e.g. gene_id, gene_symbol)
gene_id<- sub('\".*', '', gene_id, perl=TRUE)
gtf$gene_id<- gene_id

## All features in the GTF file for each DE gene
degtf<- gtf[gtf$gene_id %in% degenes,]

## Get start and end coordinates for each DE gene
decoords<- data.frame(aggregate(degtf[, c('V1', 'V7', 'V4')], by= list(gene_id= degtf$gene_id), min),
    gene_end= aggregate(degtf$V5, by= list(gene_id= degtf$gene_id), max)$x)
Hope it helps!
Dario
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Old 09-13-2012, 08:51 AM   #5
glados
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Thank you dariober for contributing with your code! It works great!
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