Question: Which keytype from org.Mm.eg.db match the annotations in the ensembl gtf file?
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gravatar for alejandro.colaneri
14 months ago by
United States
alejandro.colaneri10 wrote:

Hi, I downloaded the following gtf file from ensembl: Mus_musculus.GRCm38.91.gtf

Using DESeq2 I got a res object that have ENSEMBL symbols on it. I want to use AnnotationDbi to further annotate my res objet with gene symbol and gene names. However I am not sure which kind of keytypes are in my res object. I was expecting either ENSEMBL OR ENSEMBLTRANS however when I look at the length of different object I found this:

length(keys(org.Mm.eg.db, keytype = "ENSEMBL"))
[1] 24420
length(keys(org.Mm.eg.db, keytype = "ENSEMBLTRANS"))
[1] 19245
 dim(res)
[1] 31379     6

There are more keys in my res object than in any of the ENSEMBL related keys from the org.Nm.eg.db object. How that is possible? Please find a brief summary of what I did:

I used the ensembl gtf file "Mus_musculus.GRCm38.91.gtf" it to create index and to run alignments with STAR

echo "STAR --runThreadN 12 --genomeDir /genome --sjdbGTFfile /Mus_musculus.GRCm38.91.gtf --readFilesIn /RNAseq/140311_UNC14-SN744_0402_AC3LB8ACX/${i}_R1.fastq.gz /${i}_R2.fastq.gz --outFileNamePrefix /star_mapping/aligments_forSalmon/${i} --outSAMtype BAM Unsorted --readFilesCommand zcat" >> $i.sub

Then I created a summarize experiment object using genomicAligments

se <- summarizeOverlaps(exonsByGene, BamFileList(bamFiles), mode="Union", singleEnd=FALSE, ignore.strand=FALSE, fragments=FALSE)

Later on I run DESeq2 to perform differential expression analysis and I got the res objetc Now I want to add genesymbol, For that I am extracting the keys in my result table with myKeys=rownames(res), however I m having problem to find out which kind of keytypes those are

Hope someone can help me Thanks ALe

org.mm.eg.db rna-seq deseq2 • 757 views
ADD COMMENTlink written 14 months ago by alejandro.colaneri10
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