Hi,
I have mRNA count files with contains IDs like ENSG00000200494 (https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000200494;r=20:16670641-16670742;t=ENST00000363624).
The ensembl website shows as noncoding part of RNAs. However, the file is supposed to contain rna-seq information related to only messenger RNA. I suspect there is something wrong during alignment with the reference transcriptome.
How do you think about it? Thank you.
1 answer
You would need to look at what kinds of RNAs are caught by your particular protocols. For instance, some protocols will capture mRNA by their poly-A tails, so you would expect to not get RNA types lacking those tails. Some RNA preps will filter away small RNA fragments, so if you want small RNA fragments, you have to use a different protocol.
You have to know what the goal of the experiment was, and what protocols were chosen for that goal.
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