I'm working with a tetraploid soybean species, and I want to determine which DNA-seq reads exist on only one of the two diploid progenitor genomes. I have two consensus fasta files (one for each diploid genome) and want to map reads to them to determine which reads map to only one genome based on mapping scores. I already have a pipeline for accomplishing this, but I'm running into a problem. One consensus file has 30 million more Ns than the other. Reads that should map equally to both species favor one because it has fewer Ns, and therefore a higher mapping score. Is there a way to replace A/C/G/T's in one consensus file with an N where the other consensus file has an N? The consensus sequences were made by mapping RNA-seq and DNA-seq reads to the Glycine max genome, so they should be comparable.
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I'm not aware of a ready-made tool to do this job but it sounds like something you could do with Perl. I'm sure there are online tutorials you could use otherwise I found this book useful when first starting (http://shop.oreilly.com/product/9780596000806.do)
Are both consensus sequences the same length for each chromosome/scaffold? Doesn't really matter if they aren't, would just make the perl script to do this job easier. -
Ah, I guess I'll just have to build up my Perl skills. Probably a good idea, anyway. And yes, the consensus sequences are the same size, so it shouldn't be too difficult.
Thanks for your help!Comment
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
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