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There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2]
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Hi, I emailed them and did get the bed file! Thank you so much.
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does this work with a single .bed file?
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![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
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I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
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I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
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FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
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AFAIK "MANE" project is only for human protein-coding genes.
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