16s rRNA Sequencing Analysis and Visualization

Following the data preparation, this video attempt to outline some simple analysis in microbiome analysis and how it can be done simply with a wide varieties of tools.
Email: [e-mail]
Website: www.liquidbrain.org/videos
Patreon: / liquidbrain
Github: github.com/brandonyph/LiquidB...
MiSeq SOP: mothur.org/wiki/miseq_sop/
MEGAN6: computomics.com/services/mega...
Galaxy: usegalaxy.org/
Chapters:
0:00 Introduction
0:33 Inputs required
1:13 Analyses Included in this video
2:21 Goals for this video
4:23 Looking at the input files format
7:57 OTU identification and clustering
12:00 Phylotype Analysis
13:59 Alpha and Beta Diversity
19:25 PCA output in R
21:47 AMOVA between treatments
25:47 ggtree for tree plotting in R
29:10 Customization of ggtree
33:10 Galaxy + Krona
36:50 MEGAN6
41:35 Closing summary

[@mahbubanam2683]

Thanks for the contents❤ Galaxy and Megan just blew my mind!!! Have done most of the visualizations on plotting softwares until now 😬

[@hanesh8483]

This is brilliant thank you! I am struggling with my bachelor thesis because I don't know how to visualize my data because there are so many ways and this gives me a great overview of what is important!

[@putbassboi]

Great video!

[@dohanpramudia93]

thank you very much,

[@enriquep4857]

Nice video. It will be amazing if you make a video about create nice graphs using phyloseq.

[@WinnifredDuk]

Great video. You have video of how to create primers?

[@mostafaismail4253]

ATAC seq and CHIP-seq please ❤️❤️❤️, but great video bro ❤️❤️❤️

[@ebrahimshokoohi6372]

Thank you very much. How do you import your files to Rstudio? As you said we have three files by name final. I would really appreciate it if you assist

[@nuriar4314]

Thanks for the video, it is really useful!! It would have been nice if you showed the imported count_table like you did with the taxonomy file because you used a final.full.count_table that is not produced with the Mothur SOP, is it?? I think a few of us are struggling with the comment lines in the count_table in mothur. Any advice is greatly appreciated 🙃

[@selfstudyplan840]

Thank you a bunch . please I need you help about this segment of code
count_high 100,]
count_high2

[@rabiaejaz7717]

kindly tell me which command is used to separate taxonomy into kingdom, phylum, class, order, genus and species

[@LiquidBrain]

Depends on which command you are running on and which stages are you in during the analysis. If you already have a table dplyr::filter () will work just fine :)

[@crackers0413]

Hi, there were a few errors in the code which I can't find solutions to online:
Error in read_delim("final.full.count_table", delim = "\t", escape_double = FALSE, :
could not find function "read_delim"
Warning in install.packages :
package ‘ggtree’ is not available for this version of R
Warning in install.packages :
package ‘treeio’ is not available for this version of R
If anyone has experience with these issues, please comment

[@himalipandhi9624]

what if i am not using Miseq particularly?

[@TekkoNet]

I don't see the github page in your description!

[@LiquidBrain]

Oops, just added that. You should be able to find it now

[@TekkoNet]

@@LiquidBrain Thank you!!

[@cindelynvaldovinos6101]

p͓̽r͓̽o͓̽m͓̽o͓̽s͓̽m͓̽ 🌟