GC bias in small RNA-seq data
Hello everyone. I am dealing with small RNA seq data to extract information on miRNAs and other small RNAs. I was wondering if there is a tool (python/R based or any other pipeline) or any other way to check out GC bias as well as PCR artifacts in small RNAseq data. I was reading about Alpine tool. But there are no studies of this tool for small RNAseq data (really small: 21nt).
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FastQC does all of this... https://github.com/s-andrews/FastQC
Yeah, i checked that. I was thinking if there is any other way too or specific tool for it. Also, I want to ask, once I know specific reads showing bias, what is the next step? I mean do we exclude those reads or there is a way to rectify them?