Detecting GC Bias in Transcriptomes (RNA-seq)
What's the best way to detect GC bias in a transcriptome (RNA-seq)?
We are currently aligning to a regular genome fasta file (like hg38) but that means there are skips in the coverage. exon -- intron -- exon..... I know how to calculate GC bias of individual exons. Bedtools and R is a huge help there. But I'm stumped on how to do it for entire transcript. Any ideas?
I know how to do GC bias with Whole genome (CollectGcBiasMetrics Picard) and Sequence capture (custom scripting). But this transcript stuff is a bit more complex.
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Would it be informative to calculate the GC content of the reads themselves?
What is the final goal? Differential analysis? Check the
alpinepackage at Bioconductor which implements GC bias correction.salmonimplements this method in its--gcBiasflag if you choose it to quantify your reads agsinst a transcriptome.Appart from ATpoint's points (sorry for the pun - could not resist) you can also take a look at the R pakage cqn which have methods for identifying and correcting genome-wide GC-bias.