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Old 02-07-2014, 12:04 PM   #1
fabrice
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Location: paris

Join Date: Oct 2009
Posts: 86
Default How to get gene symbol after deseq?

Dear experts,

After I have run deseq, I got a list of genes. They are something like as follow.

> resSig[,1]
[1] "ENSMUSG00000022150+ENSMUSG00000079102:009"
[2] "ENSMUSG00000026727:016"
[3] "ENSMUSG00000026727:004"
[4] "ENSMUSG00000022150+ENSMUSG00000079102:015"
[5] "ENSMUSG00000025730:010"
[6] "ENSMUSG00000005836:007"
[7] "ENSMUSG00000073139:001"

How can I get back the gene symbol for each ID?

Thank you very much in advance.
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Old 02-11-2014, 11:40 AM   #2
thanhhoang
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Location: Ohio, USA

Join Date: Jul 2013
Posts: 16
Default

Hi,
When counting mapped reads using HTseq, you need to use gene symbol insteads of gene_id (this is default)
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Old 02-12-2014, 01:11 PM   #3
santhilalsubhash
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Location: Gothenburg, Sweden

Join Date: May 2012
Posts: 19
Default Use merge with your annotation and edgeR or DESeq result files.

Quote:
Originally Posted by fabrice View Post
Dear experts,

After I have run deseq, I got a list of genes. They are something like as follow.

> resSig[,1]
[1] "ENSMUSG00000022150+ENSMUSG00000079102:009"
[2] "ENSMUSG00000026727:016"
[3] "ENSMUSG00000026727:004"
[4] "ENSMUSG00000022150+ENSMUSG00000079102:015"
[5] "ENSMUSG00000025730:010"
[6] "ENSMUSG00000005836:007"
[7] "ENSMUSG00000073139:001"

How can I get back the gene symbol for each ID?

Thank you very much in advance.
If you have annotation file you can try merging the columns using column names.

I have also attached sample input and sample output files.


dbs <- read.table("sample_annotation.txt", header=TRUE)
resR <- read.table(edgeR_results.txt,header=TRUE)
newy <- cbind(rownames(resR),resR)
colnames(newy)[1] <- "ID"
annotated <- merge( dbs, newy, by='ID')
write.table(annotated,edgeR_results_annotated.txt,sep=" \t")


I hope this will help you.
Attached Files
File Type: txt sample_anotation.txt (98 Bytes, 2 views)
File Type: txt edgeR_results.txt (200 Bytes, 1 views)
File Type: txt edgeR_results_annotated.txt (212 Bytes, 3 views)
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