Adding two new presentations by heylf · Pull Request #57 · StreetScienceCommunity/StreetScienceCommunity.github.io

heylf · 2019-10-14T10:07:05Z

Bioinfroamtics presentation and Nanopore Sequencing presentation

bebatut

Thanks a lot @heylf 😄
I put some comments and some suggestions. Let me know if you need any help or you want to discuss about them

bebatut · 2019-12-05T12:38:38Z

_materials/1_introduction.html

+
+---
+
+### Schedule


I would not put the schedule here (but in the handbook), because we could use the slides not only for a 2-days workshop and also we are not sure about the timing

bebatut · 2019-12-05T12:43:01Z

_materials/1_introduction.html

-### Data analysis
+### Data analysis
+
+<img src="/images/materials/bioinformatics/3.svg" width="400">


This image is not really true. Most of the time we do not have the reference genome of the bacteria, so we look for the closest relatives. And we do not really care where it maps on the reference.
What we are more interesting is to identify a taxonomic assignation for the reads

bebatut · 2019-12-05T12:43:47Z

_materials/2_nanopore_sequencing.html

@@ -0,0 +1,32 @@
+---
+layout: slides
+title: "What is Nanopore-Sequencing?"


Suggested change

title: "What is Nanopore-Sequencing?"

title: "What is Nanopore Sequencing?"

bebatut · 2019-12-05T12:46:05Z

_materials/2_nanopore_sequencing.html

+### How to Read DNA
+
+
+[Video](https://nanoporetech.com/applications/dna-nanopore-sequencing)


Suggested change

[Video](https://nanoporetech.com/applications/dna-nanopore-sequencing)

<iframe src="https://player.vimeo.com/video/337258910" width="640" height="360" frameborder="0" allow="autoplay; fullscreen" allowfullscreen></iframe>

<p><a href="https://vimeo.com/337258910">Animation: Nanopore sequencing</a> from <a href="https://vimeo.com/user5318092">Oxford Nanopore</a> on <a href="https://vimeo.com">Vimeo</a>.</p>

bebatut · 2019-12-05T12:46:45Z

_materials/4_nanopore_sequencing_extended.html

@@ -0,0 +1,42 @@
+---
+layout: slides
+title: "Further Imformation about Nanopore-Sequencing"


Suggested change

title: "Further Imformation about Nanopore-Sequencing"

title: "Further Information about Nanopore Sequencing"

bebatut · 2019-12-05T12:59:51Z

_materials/2_nanopore_sequencing.html

+
+- **Fragmentation Mix (FRA):** Ligases (Exonucleases) to cut DNA into shorter pieces. Will cut at certain sequences.
+- **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand.
+- **Flush Tether (FLT):** Guides the motorprotein to the pores.


Suggested change

- **Flush Tether (FLT):** Guides the motorprotein to the pores.

- **Flush Tether (FLT)** to guide the motorprotein to the pores

bebatut · 2019-12-05T13:00:08Z

_materials/2_nanopore_sequencing.html

+- **Fragmentation Mix (FRA):** Ligases (Exonucleases) to cut DNA into shorter pieces. Will cut at certain sequences.
+- **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand.
+- **Flush Tether (FLT):** Guides the motorprotein to the pores.
+- **Seqeuncing Buffer (SQB):** For the ionic current.


Suggested change

- **Seqeuncing Buffer (SQB):** For the ionic current.

- **Sequencing Buffer (SQB)** to conduct the ionic current

bebatut · 2019-12-05T13:02:16Z

_materials/2_nanopore_sequencing.html

+- **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand.
+- **Flush Tether (FLT):** Guides the motorprotein to the pores.
+- **Seqeuncing Buffer (SQB):** For the ionic current.
+- **Flush Buffer (FB):** For washing.


Suggested change

- **Flush Buffer (FB):** For washing.

- **Flush Buffer (FB)** to wash

bebatut · 2019-12-05T13:02:56Z

_materials/2_nanopore_sequencing.html

+- **Flush Tether (FLT):** Guides the motorprotein to the pores.
+- **Seqeuncing Buffer (SQB):** For the ionic current.
+- **Flush Buffer (FB):** For washing.
+- **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell.


Suggested change

- **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell.

- **Loading Beads (LB)** to increase the molecular weight of the DNA

It helps to suck the DNA from the loading port into the flowcell

bebatut · 2019-12-05T13:04:41Z

_materials/4_nanopore_sequencing_extended.html

@@ -0,0 +1,42 @@
+---


As the content here is mostly text, not slides, we could maybe move it to the Sequencing protocol as a comment for the teachers

mmiladi · 2020-09-29T10:49:14Z

@heylf @bebatut Suggestions to change look good to me. Could either of you please just accept them and merge this PR?

heylf · 2020-10-08T13:52:14Z

I did the changes. PR can be merged if there is furhter requests.

mmiladi · 2020-10-08T17:12:41Z

_materials/4_nanopore_sequencing_extended.html

- The quality of the reads decreases at the end of a read like in Illumina Sequencing.
- Average length 2-10 kb reads. Error Rate 15-40%.
+- The quality of the reads not decreases at the end of a read like in Illumina Sequencing.
+- Average length 2-10 kb reads. Error Rate 15-40% (which comes mostly from the basecalling).


Error rate is <10% nowadays, ~5-6%.

I have changed it!

mmiladi · 2020-10-08T17:13:56Z

Thanks much @heylf . I added a single comment.

heylf added 4 commits October 11, 2019 17:10

Adding new presentations and pictures

8ac244e

Changest to slides

e8272aa

Adding new image for bioinformatics presentation

ce13d4f

Changes to presentations and material

246c6a5

bebatut reviewed Dec 5, 2019

View reviewed changes

mmiladi mentioned this pull request Sep 29, 2020

Open Pull requests #68

Open

Changes to slides and images

7f14eb5

mmiladi reviewed Oct 8, 2020

View reviewed changes

Changes to 4_Nanpopre_Seq_Extended

2538a2e

	title: "What is Nanopore-Sequencing?"
	title: "What is Nanopore Sequencing?"

		### How to Read DNA


		[Video](https://nanoporetech.com/applications/dna-nanopore-sequencing)

	[Video](https://nanoporetech.com/applications/dna-nanopore-sequencing)
	<iframe src="https://player.vimeo.com/video/337258910" width="640" height="360" frameborder="0" allow="autoplay; fullscreen" allowfullscreen></iframe>
	<p><a href="https://vimeo.com/337258910">Animation: Nanopore sequencing</a> from <a href="https://vimeo.com/user5318092">Oxford Nanopore</a> on <a href="https://vimeo.com">Vimeo</a>.</p>

	title: "Further Imformation about Nanopore-Sequencing"
	title: "Further Information about Nanopore Sequencing"

	- Flush Tether (FLT): Guides the motorprotein to the pores.
	- Flush Tether (FLT) to guide the motorprotein to the pores

	- Seqeuncing Buffer (SQB): For the ionic current.
	- Sequencing Buffer (SQB) to conduct the ionic current

	- Flush Buffer (FB): For washing.
	- Flush Buffer (FB) to wash

-- **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell.
+- **Loading Beads (LB)** to increase the molecular weight of the DNA
+   It helps to suck the DNA from the loading port into the flowcell

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heylf commented Oct 14, 2019

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mmiladi commented Sep 29, 2020

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heylf commented Oct 8, 2020

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mmiladi commented Oct 8, 2020

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