Genome and Transcriptome as a reference
Hello,
I have mapped RNA-Seq data with human genome and transcriptome. I observed there is a great difference between the overall mapping percent. The overall mapping percent with transcriptome as a reference is very less than overall mapping percent with genome as a reference.
Could someone help me understand the reason why this is so?
Thank you in advance.
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It is quite possible that your RNA-seq library prep generated many reads that are outside of the regions specified by the CDS transcriptome reference FASTA that you're using.
Out of curiosity: What is your transcriptome reference? GENCODE's is the most complete (https://www.gencodegenes.org/releases/current.html - see the section on Fasta files).
I have downloaded from:
RefSeq Transcripts
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