Hi Bioinformatics lovers,

I turned 38 this week. I typed my first "hello world" 12 years ago. I wrote it down in my first programming book: Python Programming for the Absolute Beginner.

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I have written a post on re-inventing yourself https://lnkd.in/eC_ChYst If you do not go out of your comfort zone, you will never grow.
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However, the growth will take time, sometimes taking a decade. But if you focus on doing small things consistently, you will see the success https://lnkd.in/eyuSRAGA​
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If you are still in doubt of yourself, stop it. Embrace the challenges as that's the only way you can learn and grow. Keep asking are you learning new things? Are you telling yourself silly stories that prevent you from improving yourself?
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Now, let's switch gears to talk about automation:

If you find repeating the same code by copying and pasting, If you find yourself doing the same task daily, it is time to automate them by using functions and writing shell scripts.

In R, once you master the purrr::map() function, your life is much easier. If you have a spreadsheet with multiple tabs, how can you read all of them in to R efficiently and combine them into a single dataframe? Check out this video I made for you:

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Other resources from this week:

1. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03252-4​
2. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics https://www.nature.com/articles/s41576-020-0265-5​
3. Principles and therapeutic applications of adaptive immunity https://www.cell.com/cell/fulltext/S0092-8674(24)00353-2​
4. ​Exploring Transcription factor Binding with UCSC Genome Browser​
5. Obtain metadata for public datasets in GEO https://divingintogeneticsandgenomics.com/post/obtain-metadata-for-public-datasets-in-geo/​
6. fastq-dl https://github.com/rpetit3/fastq-dl Download FASTQ files from the European Nucleotide Archive or the Sequence Read Archive repositories.
7. PICsnATAC to accurately quantify snATAC-seq data https://github.com/Zhen-Miao/PIC-snATAC​
8. ​How to Process Single Cell RNAseq with 2 lines of code from fastq to count matrix​
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Happy Learning!

Tommy

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DNA confesses Data speak

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Let's connect on twitter and Linkedin!

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