Transmictomic analysis with draft reference genome

Question

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Hello, ultra noob here but is it possible to perform a transcriptome analysis but using a draft genome as a reference? I'm working with an assembled draft genome (a fasta file with a bunch of contigs) and I have no clue if bowtie or the like will work on this reference.

[rpolicastro]

😺 How many contigs do you have? I've had difficulty in the past using highly fragmented genomes (10k+ contigs) with tools like STAR.

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About 24 nowhere close to that high, bacterial genome if that helps.. :O

Answer 1

[rpolicastro]

🐅 That's less contigs than some genomes have chromosomes, so you should be fine! Assuming it has decent coverage and the annotation is fairly accurate of course.

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Thanks! I'll give it a go see how it turns out :)