GC content
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Matilde • 0
@4fc332c0
Last seen 6 weeks ago
Portugal

Hello,

I am trying to do normalization of genes and I only have the counts from RNA- seq. I want to get my GC content so that I can use the function getGeneLengthAndGCContent from EDAseq, however as I only have the counts, I don't know how can I use it.

Thank you

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session

sessionInfo( )

EDASeq • 115 views
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Robert Castelo ★ 2.9k
@rcastelo
Last seen 10 days ago
Barcelona/Universitat Pompeu Fabra

hi,

The help page of getGeneLengthAndGCContent() says that this function "Automatically retrieves gene length and GC-content information from Biomart or org.db packages", so this function is gives you the GC content, given a vector of gene identifiers. So, in principle you need to put the gene identifiers of your table of counts (probably stored as the row names of that table) into a vector and call this function with that vector as its first argument. Please read carefully its help page and try to be more specific about what part of that help page you do not understand.