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.