add RNASeqTools TSS tutorial

[maltesie]

RNASeqTools TSS tutorial notebook

Types of changes

This PR implements the following changes:

• [x] :sparkles: New feature (A non-breaking change which adds functionality).
• [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
• [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).

:clipboard: Additional detail

The existing RNASeq tutorial is outdated and the new one showcases parts of the RNASeqTools package. The notebook should run by itself.

The tutorial 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

:ballot_box_with_check: Checklist

• [ ] :art: The changes implemented is consistent with the julia style guide.
• [ ] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
• [ ] :blue_book: I have added or updated relevant user and developer manuals/documentation in docs/src/.
• [ ] :ok: There are unit tests that cover the code changes I have made.
• [ ] :ok: The unit tests cover my code changes AND they pass.
• [ ] :pencil: I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
• [x] :ok: All changes should be compatible with the latest stable version of Julia.
• [x] :thought_balloon: I have commented liberally for any complex pieces of internal code.

[maltesie]

Thanks a lot already for the review. I will look into packaging the binary dependencies and fix the comments style consistently in the next days :)

[maltesie]

Hi @kescobo

Sorry for the long delay, I couldn't find the time to work on this. Today I managed to make an artifact for one of my dependencies, bwa-mem2: https://github.com/maltesie/bwamem2_jll.jl

I'm working on setting up binary packages for sra-tools and fastp (nearly through) as well. Will let you know when I'm done :)

I didn't adjust any code in RNASeqTools yet to actually use the artifacts, though. I hope I can do this over the weekend.

[maltesie]

bwamem2_jll is now a registered binary package and I adjusted RNASeqTools to use it. But I cant get sra-tools to compile with BinaryBuilder. I will check how to use BioServices more for downloading, and otherwise check if I can use CondaPkg for that as you suggested. I hope I can update the notebook during the next week.

[kescobo]

Rad! CC @M-PERSIC - might be an opportunity to team up here

[M-PERSIC]

Hi @maltesie! Yesterday I announced the BioJuliaDocs initiative, which is a project for creating a centralized landing page for BioJulia with tutorials and code snippets. This might deprecate the need for a separate BioTutorials package as we would include any relevant examples into the site.
I'd love to collaborate with you on updating some examples to be included. You can reach out to me on the BioJuliaDocs repo linked above or we can discuss on Slack at the #biology channel with other community members or even privately at my email address.