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To save the output of `samtools flagstat` in a table format, you can use the `-O` option followed by `tsv` to select the tab-separated values format. This format is suitable for importing into spreadsheet software. Here's an example command that demonstrates how to use this option:

```bash
samtools flagstat -O tsv in.bam > output.tsv
```

This command will generate a `.tsv` file named `output.tsv` with the flagstat output in a tab-separated format, which you can then open with any program that supports TSV files, such as Excel or Google Sheets¹[1].

Source : conversation avec Bing, 27/04/2024
(1) samtools-flagstat(1) manual page. http://www.htslib.org/doc/samtools-flagstat.html.
(2) flagstat machine readable output format · Issue #1077 · samtools .... https://github.com/samtools/samtools/issues/1077.
(3) samtools-flagstat(1) — samtools — Debian unstable — Debian Manpages. https://manpages.debian.org/unstable/samtools/samtools-flagstat.1.en.html.
(4) Ubuntu Manpage: samtools-flagstat - counts the number of alignments for .... https://manpages.ubuntu.com/manpages/jammy/man1/samtools-flagstat.1.html.
(5) undefined. https://samtools.github.io/hts-specs/SAMv1.pdf.
(6) undefined. https://www.json.org/.

samtools-flagstat(1) manual page Samtools

ANOVA (Analysis of Variance) and Tukey's HSD (Honestly Significant Difference) test are commonly used in scientific papers even when the data are not normalized because these methods are robust to certain violations of their assumptions. ANOVA is particularly robust to non-normality when sample sizes are equal or large, which tends to mitigate the effects of non-normal distributions¹[4].

The central limit theorem supports this robustness, suggesting that with a sufficiently large sample size, the distribution of the sample means will approximate a normal distribution, even if the underlying population distribution is not normal. This allows ANOVA to produce reliable results despite non-normality in the data.

Tukey's HSD test is often used in conjunction with ANOVA as a post hoc analysis to determine which specific group differences are significant. It controls for the family-wise error rate, which is the probability of making one or more Type I errors when performing multiple comparisons²[5].

However, it's important to note that if the data are heavily skewed or have outliers, transformations or non-parametric alternatives might be more appropriate. Non-parametric equivalents, like the Kruskal-Wallis test, can be used when the assumptions of ANOVA are not met, and for post hoc comparisons, the Dunn's test can serve as a non-parametric counterpart to Tukey's HSD³[7].

In practice, researchers may choose ANOVA and Tukey's HSD for their simplicity and the availability of software that supports these tests. They also may be following conventions within their field or the expectations of peer reviewers and journals. Nonetheless, it's crucial for researchers to justify their choice of statistical methods and ensure that the assumptions underlying these methods are reasonably met in their data. If there's significant deviation from these assumptions, alternative methods should be considered.

Source : conversation avec Bing, 27/04/2024
(1) Can I trust ANOVA results for a non-normally distributed DV?. https://stats.stackexchange.com/questions/5680/can-i-trust-anova-results-for-a-non-normally-distributed-dv.
(2) A Guide to Using Post Hoc Tests with ANOVA - Statology. https://www.statology.org/anova-post-hoc-tests/.
(3) Is there a nonparametric equivalent of Tukey HSD?. https://stats.stackexchange.com/questions/17342/is-there-a-nonparametric-equivalent-of-tukey-hsd.
(4) ANOVA with Tukey's HSD Post Hoc Test in SPSS. https://www.youtube.com/watch?v=JiyeE7uzSbQ.
(5) Tukey Method - One-Way ANOVA. https://www.youtube.com/watch?v=zQr190cacC0.
(6) ANOVA : TWO FACTOR WITH REPLICATION & TUKEY TEST ON EXCEL. https://www.youtube.com/watch?v=3-nRXmq-Zng.
(7) Tukey's test of additivity - Wikipedia. https://en.wikipedia.org/wiki/Tukey%27s_test_of_additivity.
(8) What Is the Tukey HSD Test? | Sciencing. https://sciencing.com/what-is-the-tukey-hsd-test-12751748.html.

ANOVA with Tukey's HSD Post Hoc Test in SPSS This video demonstrates how to conduct an ANOVA with a Tukey’s HSD post hoc test in SPSS. The results of pairwise comparisons with a Bonferroni correction ar...

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We are pleased to inform you that we extend the Abstract submission deadline to November, 10th 2023.
Pleased find attached the confirmed speakers 🔊
https://lnkd.in/ew9QfddF
Harry up ! we are waiting for you in Hammamet, Tunisia

🛑📣The Tunisian Society of Microbial Ecology (ATEM) is thrilled to announce its fourth International Conference on Microbial Ecology, ATEM’23, jointly organized with the inaugural Congress of the "Sciences Horizons Association" (ASHO). This collaborative scientific event, which will take place from 7th to 10th December 2023, at Belisaire Hotel, (Hammamet, Tunisia), will unite researchers from diverse nations, all converging at the nexus of microbial ecology, where chemistry and biology harmoniouslyintersect. Supported by a vibrant cadre of early-career scientists, the organizers infuse the event with unlimited enthusiasm and dedication, fostering fresh ideas, novel goals, and innovative approaches.
Under the theme "From Microbial Lifestyle to Styling Ecosystems," we revisit our inaugural 2013 conference's essence, exploring microbial diversity, challenges, and applications. As life and biodiversity mature, so does our understanding of genes, genomes, and environments. In the current “Omics” era, microbial ecology unfolds anew, offering fresh insights into ecosystem dynamics and drawing the interest of a new generation of researchers.
Our commitment to cooperation remains solid, and esteemed invited speakers support this unity. We are also thrilled to have the support of the International Society of Microbial Ecology (ISME).
For detailed information about our invited speakers, the scientific and organizing committees and how to participate, please register through the following link: https://docs.google.com/forms/d/e/1FAIpQLSd56SnyFmripSiiB7muP60rVe5F4mq6h_yUtJteeuUMgLwt1g/viewform?usp=pp_url

Important dates:
- Abstract submission Deadline: October 31st, 2023
- Acceptance notification: November 7th, 2023
We eagerly anticipate your participation and contributions to make ATEM'23 a resounding success. Join us in Hammamet, Tunisia, to explore the fascinating world of microbial ecology.
If you have any inquiries or require further information, please do not hesitate to reach out. Let's make this event a memorable gathering of scientific minds.