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assign Ensemble gene ids to transcripts

3

in the RNA seq tutorial in this code block ```R txdb

HadrienG

1) Mapping tutorial docs were asking for *.gz files when there were none present. 2) `mpileup` has been migrated from samtools to bcftools. Command updated accordingly.

carlcrott

Bumps [pygments](https://github.com/pygments/pygments) from 2.8.1 to 2.15.0. Release notes Sourced from pygments's releases. 2.15.0 Added lexers: Carbon (#2362, #2365, #2366, #2367, #2368, #2369, #2370) Dax (#2335, #2345) MediaWiki Wikitext (#2373, #827)...

dependabot[bot]

Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.1 to 6.3.2. Changelog Sourced from tornado's changelog. Release notes .. toctree:: :maxdepth: 2 releases/v6.3.2 releases/v6.3.1 releases/v6.3.0 releases/v6.2.0 releases/v6.1.0 releases/v6.0.4 releases/v6.0.3 releases/v6.0.2 releases/v6.0.1 releases/v6.0.0 releases/v5.1.1 releases/v5.1.0 releases/v5.0.2...

dependabot[bot]

Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 8.1.1 to 10.0. Release notes Sourced from pymdown-extensions's releases. 10.0 Break: Snippets: snippets will restrict snippets to ensure they are under the base_path preventing snippets relative to...

dependabot[bot]

In the [Aligning Reads section](https://www.hadriengourle.com/tutorials/mapping/#aligning-reads) , the command is listed as: ```bash bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq.gz \ -2 SRR957824_trimmed_R2.fastq.gz -S SRR957824.sam ``` However, `.gz` compressed files were not generated...

pichaelpayne

Bumps [mkdocs](https://github.com/mkdocs/mkdocs) from 1.0.4 to 1.1.2. Commits ff0b726 Bump version to 1.1.2. 58d70c2 Normalize IP addresses and change error to warning 85b3bef Bump version to 1.1.1. 0d17a52 Flake8 cleanup. fa5aa4a...

dependabot-preview[bot]

Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 4.4.0 to 4.6.3. Release notes Sourced from mkdocs-material's releases. mkdocs-material-4.6.3 Removed optional third-party plugins from requirements.txt Updated Docker image to contain all supported third-party plugins mkdocs-material-4.6.2 Added...

dependabot-preview[bot]

The mummer part needs to be changed (ex: no --png option)

jhayer

update assembly tuto

1

We need to update the Busco part to quast -b instead (with dl of the bacterial db, file renaming of the tar.gz). Maybe we could add a part in the...

jhayer