RNA-seq: bias in coverage
When I observe mapped reads of RNA-seq data, I realize that many genes have the first exon not covered. I just read this seems to be a bias due to CpG content, first exons are usually CpG island, so... My question is, how is it possible to avoid this bias?
Could someone also tell me why the coverage of the last exon-3'UTR is so high compared to the other exons? This is visible for all the genes!
Many thanks to all who will replay.
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angela.sparago •
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Was the library prepared using polyA enrichment? If the RNA is damaged, it's possible you get a bias against the 5' end.
I'm not sure you can really avoid the bias. If exon 1 on average has significantly higher CG content than exon N, then thats just the fact of the matter.