Question: PAM50 subtyping RNA-Seq nested gene
gravatar for rpraveenkumarbio
2.8 years ago by
United States
rpraveenkumarbio10 wrote:

Planning to do breast cancer subtyping based on PAM50 model using RNA-Seq data.

The conundrum I am facing is that one of the 'PAM50' gene “MIA” is annotated as nested in "ensembl-84. The annotation is that "MIA" is nested in a long gene “MIA-RAB4B”. Hence all the reads mapped to MIA are regarded ambiguous. This is like the last case in the HTSeq example here

Any suggestions are welcome. Should you suggest me to go with Data (no MIA counts) as it is or get-rid of long gene “MIA-RAB4B” in the annotation file to get MIA counts for the sake of subtyping.

rna-seq genefu gene genome • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 2.8 years ago by rpraveenkumarbio10
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