Update RNAseq tutorial #5

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1. maltesie commented on Apr 16, 2023

   

   maltesie

   on Apr 16, 2023

   Last edited by maltesie

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   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
2. kescobo commented on Apr 17, 2023

   

   kescobo

   on Apr 17, 2023

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   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:

   
3. kescobo commented on Apr 18, 2023

   

   kescobo

   on Apr 18, 2023

   MemberAuthor

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   (if you'd like, I can kick off the PR from your fork, but it's good practice :-) )
4. maltesie commented on Apr 18, 2023

   

   maltesie

   on Apr 18, 2023

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

   linked a pull request that will close this issueadd RNASeqTools TSS tutorial #10on Apr 19, 2023