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Add microGalaxy tag to tnseq tutorial #4798

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Mar 18, 2024
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Add microGalaxy tag to tnseq tutorial #4798

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1 change: 1 addition & 0 deletions topics/genome-annotation/tutorials/tnseq/tutorial.md
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Expand Up @@ -7,6 +7,7 @@
- bacteria
- tnseq
- essential genes
- microgalaxy
questions:
- "What is Transposon insertion Sequencing?"
- "How to get TA sites Coverage ? "
Expand Down Expand Up @@ -593,7 +594,7 @@
## Transit
Transit is a software that can be used to analyse TnSeq Data. It is compatible with Mariner and Tn5 transposon. In total, 3 methods are available to assess gene essentiality in one sample.

#### Gumbel method

Check failure on line 597 in topics/genome-annotation/tutorials/tnseq/tutorial.md

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[rdjsonl] reported by reviewdog 🐶
You have skipped a heading level, please correct this.
<details><summary>Listing of Heading Levels</summary>

```
## Transposon insertion Sequencing
## Building a TnSeq library
## Tnseq analysis
# Data upload
# Remove all non genomic sequences from the sequenced reads
## Separate reads by experimental conditions
## Remove Adapter sequence
## Separate reads from different transposon constructs
## Remove the remaining transposon sequence
# Count the number of insertion per TA sites
## Align the reads to a reference genome
## Compute coverage of the genome
## Identify TA sites positions
## Merge overall coverage and positions of TA sites to get the coverage of each TA sites
# Predicting Essential Genes with Transit
## Transit
#### Gumbel method
#### HMM method
#### Tn5Gaps method
## Predict the essentiality of genes
## Compare the essential genes between two conditions
# Conclusion
```
</details>

Raw Output:
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The Gumbel method performs a gene by gene analysis of essentiality for Mariner data based on the longest consecutive sequence of TA site without insertions in a gene. This allows to identify essential domains regardless of insertion at other location of the gene.

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