16s rRNA Sequencing Analysis | Mothur Walkthrough Part 1

Рет қаралды 11,777

2 жыл бұрын

Following the 5 years anniversary of the channel, I am remaking the pipeline that I made during my trip to Taiwan in 2016. This tools is still being actively updated with more advance tools. but the underlaying core remain unchanged, it is still free, open sources and designed to be the one-for-all analysis tools in any platforms.
In Part 1, I try to go through the process on how the properly import and analysis the data following the walkthrough on their website, until I got a fasta+count table+taxonomy file.
Mothur SOP website
mothur.org/wiki/miseq_sop/
Email: liquidbrain.r@gmail.com
Website: www.liquidbrain.org/videos
Patreon: / liquidbrain
github: github.com/brandonyph/LiquidB...

Пікірлер: 28

@belajarbiologi9839 4 ай бұрын

This is very nice,,thank you very much for kindly making this tutorial

@ericagardner8249 Жыл бұрын

Thank you so much for this video!

@suranjanasikdar6556 Жыл бұрын

Hello i have antibiotic resistance gene (7 different tet gene) sequences. How I can analyse that? Can I see the OTU or that kind of analysis using just the NCBI fastq data? I want like bacteial community analysis of each gene. but I dont have any numbers. How I can proceed?

@tamizhiniloganathan9708 Жыл бұрын

Hello sir,nice video.I have small query about hypervariable region.The tutorial reference uses V4 region.How about creating the new reference for different hypervariable region like V3 and V4 or combined region.Please help me with it sir

@saranyasweet Жыл бұрын

Hi while trying chimera.vsearch step for our sample data.. it s showing vsearch file does not exist. But the file is inside the working directory.. can u tell how to sort this out

@williamvilchezcruz 5 ай бұрын

Very nice the video

@DrdoaaEl-hadedy Жыл бұрын

why i canot find qual file after make.contigs(file=stability.files) i use 1.48 version of mothur

@foodie_0456 Жыл бұрын

Hi, the data above shows pairwise data layout. Do you have a tutorial for Processing MiSeq single (unpaired) reads.

@LiquidBrain Жыл бұрын

If you dont have a large number of sample, you can follow the site on the make.contigs() command and skip the make.files() directly Otherwise you can actually use the same make.file() command on your sample list directly as long as you have the correct naming scheme i.e. L001_R1_001.fastq ... Ref mothur.org/wiki/make.contigs/ mothur.org/wiki/make.file/

@MfundoG Жыл бұрын

Hi! Thanks for the tutorial The make.contigs command gives me an error- using 2 processors, Error: did not complete make.contigs Might this be a problem with my computer? Is it a normal Issue? How do I fix it?

@LiquidBrain Жыл бұрын

Can I check if you are using the standard input from the tutorial? Or are you using your own files?

@himalipandhi9624 10 күн бұрын

what if I am not using Miseq particularly ? and particular illumina platform is not specified when I get the data ?

@mijailc 2 жыл бұрын

Hi! Thank you very much for this tutorial, do you know where I can find trainsets for 18S?

@LiquidBrain 2 жыл бұрын

Sorry not really familiar with running 18s on a bacteria pipeline , RDP only hold database for 16s and funal 28s (rdp.cme.msu.edu/misc/resources.jsp). Do you have a paper doing something similar to yours and check which reference are they using? SILVA have some ref on eucaryotic SSU (www.arb-silva.de/browser/ssu/) just not sure they can be used in this scenario.

@mahbubanam2683 Жыл бұрын

Hi, I am new to this channel. Thanks for the great contents @LiquidBrain Bioinformatics. @Mijali, I worked with 18s data recently and was also looking for trainset data for eukaryotes. It seems like there is none at this moment (please share if you've found any). Instead, I used the silva.nr_v138.1 (full length database with 14,871 eukarya sequences) for the reference and taxonomy files in the classify.seqs command. It took some time to process the data since the reference file is very large, but it worked pretty well for me. Please share if you have found an easier or better way to classify the sequences.

@emilceviruel3620 2 жыл бұрын

Hi! I want to see make.biom tutorial (for functional prediction analysis) from taxonomy and OTU table (.taxonomy and .shared files)

@LiquidBrain 2 жыл бұрын

I am working on the part 2 of this series, I will remember to put this in :)

@najibabdellaoui6442 2 жыл бұрын

hello sorry to ask, is it possible to do a tutorial about analyzing lncRNA-seq?

@LiquidBrain 2 жыл бұрын

well, it's not in the plan, but i will see what I can do. Might take a while though

@mirij827 2 жыл бұрын

I am trying to run mothur, but I only have fasta files (as dataset was created via sanger sequencing) and I am not really sure how can I start as most resources start with fastq file.

@LiquidBrain 2 жыл бұрын

Well, it depends. Are those clean assembled fasta? If you are also running 16s, you can start directly from the annotations step after the assembly.

@mirij827 2 жыл бұрын

@@LiquidBrain how can I check whether fasta is assembled or not?

@LiquidBrain 2 жыл бұрын

Depends on where you got the data from~ usually from machine we will be getting a fastq and it is stored in fasta after the cleaning, filtering and assembly ... but, sometimes if you get it from a person or a company, its going to be hard to say

@johirislam8174 2 жыл бұрын

Nice one, i want to analyse DNAseq data through linux .So how can i do that??

@LiquidBrain 2 жыл бұрын

For mothur, just download the zip file form their website and run ./mothur in the terminal to enter the interactive mode~the rest should be identical to the one shown in the video :)

@johirislam8174 2 жыл бұрын

@@LiquidBrain thats great .But I want to know another thing, I want to analyse WGS,WES,tNGS data analysis through it. Expample to see the mutation,identify varient .So how can i do that. And what is the role of python in NGS data analysis

@mostafaismail4253 2 жыл бұрын

Can u make DIFFERENTIAL ATAC-SEQ , CHIP-SEQ

@LiquidBrain 2 жыл бұрын

Not sure how I can transform them into a video at the moment, Satija lab has a really good guide in multi model analysis, just not sure if this is what you are looking for at this moment (satijalab.org/signac/articles/pbmc_vignette.html)