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I have 5 sets of raw Illumina whole genome shotgun data from 5 different species, and 3 reference genomes that are assembled/annotated, I want to produce a similar table to Table S2 of this paper: https://www.sciencedirect.com/science/article/pii/S0960982221011908#app2.

This involves comparing reads from each of my 5 new genomes to each of the 3 reference genomes.

How can I go about aligning the sets of seq data to the references so I can capture the CDS, conserved noncoding elements (CNEs), miRNA, and ultraconserved noncoding elements (UCNE)?

I only have CDS annotations for the 3 reference genomes, so I will also need to annotate the miRNA, CNE, and UCNE myself. Suggestions for software to do this would be helpful.

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  • $\begingroup$ How do the reference genomes map onto the raw data you have? E.g. you have a big species complex or genus with several species, and there are 8 species, of which 3 have reference genomes? Or are some of your sequence data different isolates of the same species that you have references for? THis changes how you want to analyze the data significantly. Furthermore: what is the raw data? Is it Illumina genomic, PacBio genomic, Illumina RNA-seq, PB RNA-seq....? $\endgroup$ Apr 17 at 18:16
  • $\begingroup$ Ok looking at the table: you have 5 species, each of which you want to compare to each of 3 reference genomes- is that accurate? Also: do you have annotation tracks for the stuff you're interested in on each of your reference genomes? $\endgroup$ Apr 17 at 18:18
  • $\begingroup$ @MaximilianPress The raw data is Illumina. Yes i do have 5 species, that I want to compare to the 3 reference genomes, im working with lizard species, and the three reference are gekko japonicus, leopard gecko, and crested gecko. The CDS is annotated for each reference, but I believe there isn't miRNA info avaliable. $\endgroup$
    – JohnDoe23
    Apr 19 at 3:00

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