Question: How to interpret exon reads from recount for version 2?
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gravatar for simplitia
16 days ago by
simplitia30
simplitia30 wrote:

Dear all, I'm trying to get exon by exon data matrix. I can download the data either directly from the website or through the R package.
For example here is simple single sample example:

download_study("DRP001219", type = "rse-exon", outdir="./data/")
load(file.path( "./data/rse_exon.Rdata"))
count = assays(rse_exon)$counts

Here is how the data matrix look like. For example here is one for KRAS which should have 6 exons the most, however this is how the annotation look like. Anyone know how I can convert or annotate this with exon info specically for version 2? thanks.

                 DRR014113
ENSG00000133703.11     78483
ENSG00000133703.11      4095
ENSG00000133703.11      5518
ENSG00000133703.11       388
ENSG00000133703.11      2350
ENSG00000133703.11      5462
ENSG00000133703.11      1972
ENSG00000133703.11      2725
ENSG00000133703.11       235
ENSG00000133703.11      1108
ENSG00000133703.11      2495
ENSG00000133703.11         0
ENSG00000133703.11         0
rna-seq tcga • 75 views
ADD COMMENTlink modified 16 days ago • written 16 days ago by simplitia30
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