Update RNAseq tutorial - Githubissues

BioJulia / BioTutorials

Tutorial Notebooks of BioJulia

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Update RNAseq tutorial #5

Open kescobo opened 2 years ago

kescobo commented 2 years ago

Some work in this direction already in #2, though that's out of date now too. Also related to #3 .

maltesie commented 1 year ago

I made a draft for a new tutorial for RNAseq data. It uses reads from a TEX-treated sample in V. Cholerae and computes putative transcription start sites in it. It shows how to

download reads from SRA
align reads using bwa-mem
read .bam files and .gff files
annotate alignments with features from .gff files
compute coverage from alignments
compute maxima in the difference along the coverage as putative TSS

Does that make sense? I put everything here

kescobo commented 1 year ago

Go ahead an make a PR and we can discuss there. When you push to your fork, there should be a button that says "open pull request," but if not, you can open the pull requests tab here or on your repo, click "new PR", and then have your branch target main here:

kescobo commented 1 year ago

(if you'd like, I can kick off the PR from your fork, but it's good practice :-) )

maltesie commented 1 year ago

I created a PR, I think. Thanks for all the help :)