I have a list of Affy Probe sets and their corresponding gene symbol, does anyone know how I can convert them to the genomic coordinates of the gene so I can intersect them with my ChIP-seq peaks?
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Originally posted by ETHANol View PostI have a list of Affy Probe sets and their corresponding gene symbol, does anyone know how I can convert them to the genomic coordinates of the gene so I can intersect them with my ChIP-seq peaks?
best regards
T.
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Okay, I have the annotation file form Affymetrix (csv file) and it has the probe sets and the some genomic coordinates. My problems are two:
1) How can I match the probe sets on the data from the microarray experiment with the genomic coordinates/probe sets on the other file?
2) The genomic coordinates are not for the whole gene. How do I get the whole gene (I eventually want promoters). I think I should be able to do this with Galaxy.--------------
Ethan
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sorry I did not understand that you were looking for coordinates of genes.
for sure there are many possibilities and galaxy, which i never used, might be an option.
in case you are a bit familiar with R/bioconductor, there is a package called 'biomaRt' which is a rather easy tool to retrieve genomic coordinates of whatever and you can easily use affy probe identifiers to query.
promoter coordinates is probably more tricky because of the lack of a robust annotation but you could start with a simple approach defining the region 1-2kb upstream of the TSS as promoter (depends very much on the organism) and map your chipseq reads to those.
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R, I was afraid it would come to that. I'm trying to get going with R, but it's difficult and will take some time. BiomaRt looks like the tool I need.
Can someone help me with this. In the user guide they have instructions for getting genomic coordinates of the genes for Affy probes. I have a question about the following:
In this line specific probes are assigned to 'affyids':
affyids = c("202763_at", "209310_s_at", "207500_at")
and 'affyids' is the value used to query the data base.
Okay, that's great but I want to use a list of about 1000 Affy probes that I have as a text file ('mytextfile.txt') in the same directory that I a started R in.
Is there a command line (or two..) that I can use to assign my list of Affy probes to 'affyids'.
Sorry if my R-speak no so good.... but I'm a molecular biologist and new to the computer universe.
Thanks a billion to anyone that can help.--------------
Ethan
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If you don't want to deal with R/Bioconductor, I guess you could use the web interface of Ensembl/Biomart (http://www.biomart.org/). It's quite intuitive to use.
Nevertheless, it would be probably useful to get to grips with R. See if this bit of code helps:
Code:## Get the genome coordinates of the genes tagged by a set of ## Affymetrix probes IDs ## Assuming your file of affy probes IDs is a single column of ## probes identifiers, one probe per line, no header. ## E.g. something like this: # Ssc.25128.1.S1_at # Ssc.6614.1.S1_at # Ssc.24115.1.A1_at # Ssc.15874.1.S1_at # Ssc.30896.2.S1_at library(biomaRt) affyids<- read.table(file= 'mytextfile.txt', header=F) affyids<- as.vector(affyids[,1]) mart<- useDataset(dataset= "sscrofa_gene_ensembl", ## Change dataset here useMart("ensembl")) probe2gene<- getBM( attributes= c('affy_porcine', 'ensembl_gene_id', 'chromosome_name', 'strand', 'start_position', 'end_position'), filters= 'affy_porcine', ## Change as appropriate value= affyids, mart= mart)
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