Hi Bioinformatics lovers,

How is your weekend going? We had a leaking toilet, so it is a little hectic with three kids. Anyway, you should expect a newsletter from me every Saturday morning.

Today is a little delayed.

For those who want to learn bulk RNAseq analysis, check out these two tutorials:

1. How to preprocess GEO bulk RNAseq data with salmon https://divingintogeneticsandgenomics.com/post/how-to-preprocess-geo-bulk-rnaseq-data-with-salmon/​
2. Downstream of bulk RNAseq: read in salmon output using tximport and then DESeq2 https://divingintogeneticsandgenomics.com/post/downstream-of-bulk-rnaseq-read-in-salmon-output-using-tximport-and-then-deseq2/​

Unpopular opinion in bioinformatics from me: knowing the tools out there is more crucial than starting from scratch. Most problems you face have been tackled before. Don’t reinvent the wheel; save time by using existing tools.
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Moreover, the established packages will typically have fewer errors than a quick and dirty implementation. However, do not blindly trust any package either.
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For a comprehensive guide on staying up-to-date with the latest advancements in this field, check out my video: "6 Proven Strategies to Keep Pace with Evolving Trends in Bioinformatics" here.

Other resources from this week:

1. Bioinformaticians are impatient. Conda is notorious slow... then I found mamba https://github.com/mamba-org/mamba, then I found pixi https://prefix.dev/blog/pixi_a_fast_conda_alternative: Blazing fast cross-platform package management for teams by the creators of the mamba package manager.
2. Snakemake new feature: Updating existing output files https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#updating-existing-output-files​
3. ​Understanding the Path Variable in Unix Systems​
4. ​Align multiple ggplot2 plots by axis​
5. ​"Variant scores calculated by GATK did not clearly distinguish true positives from false positives in the vast majority of cases, implying that hard-filtering with GATK could be challenging.​
6. ​DeepSomatic is an extension of deep learning-based variant caller DeepVariant
7. ​ExpoSeq: simplified analysis of high-throughput sequencing data from antibody discovery campaigns | Bioinformatics Advances | Oxford Academic​

Happy Learning!

Tommy

DNA confesses Data speak

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Let's connect on twitter and Linkedin!

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