- 45
- 21 419
Shawn McMurtrey
United States
Приєднався 8 лис 2018
Tutorial on submitting a BUSCO job with slurm.
Here we see how to run the bioinformatics tool BUSCO on a de novo genome file. The code used in the video is listed below. Feel free to subscribe if you found this video helpful!
#genomes.txt
Coprinus_1A;/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/fasta/;/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/fasta/scaffolds.fasta
#BUSCO.sh
#!/bin/bash
#SBATCH --partition=all.q
#SBATCH -J BUSCO_Coprinus # Set the job name
#SBATCH -o BUSCO_Coprinus_output # Output files for stdout and stderr
#SBATCH -e BUSCO_Coprinus_error # Error files
MYFILE='/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/genomes.txt'
for LINE in `cat ${MYFILE}`; do
ELEMENT1=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $1}'`
echo "ELEMENT1 is: ${ELEMENT1}"
ELEMENT2=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $2}'`
echo "ELEMENT2 is: ${ELEMENT2}"
ELEMENT3=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $3}'`
echo "ELEMENT3 is: ${ELEMENT3}"
conda init
conda activate /home/bpp/mcmurtrs/nfs7/conda/miniconda3
CMD=" busco -f -i ${ELEMENT2} -l basidiomycota_odb10 -m genome -o ${ELEMENT1}_busco "
echo $CMD
eval $CMD
echo -n "Finished running BUSCO!"
done
#genomes.txt
Coprinus_1A;/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/fasta/;/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/fasta/scaffolds.fasta
#BUSCO.sh
#!/bin/bash
#SBATCH --partition=all.q
#SBATCH -J BUSCO_Coprinus # Set the job name
#SBATCH -o BUSCO_Coprinus_output # Output files for stdout and stderr
#SBATCH -e BUSCO_Coprinus_error # Error files
MYFILE='/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/genomes.txt'
for LINE in `cat ${MYFILE}`; do
ELEMENT1=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $1}'`
echo "ELEMENT1 is: ${ELEMENT1}"
ELEMENT2=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $2}'`
echo "ELEMENT2 is: ${ELEMENT2}"
ELEMENT3=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $3}'`
echo "ELEMENT3 is: ${ELEMENT3}"
conda init
conda activate /home/bpp/mcmurtrs/nfs7/conda/miniconda3
CMD=" busco -f -i ${ELEMENT2} -l basidiomycota_odb10 -m genome -o ${ELEMENT1}_busco "
echo $CMD
eval $CMD
echo -n "Finished running BUSCO!"
done
Переглядів: 35
Відео
How to use HMMER to find a gene sequence within in a full genome sequence file. Video #3.
Переглядів 1,2 тис.Рік тому
In this video we are using HMMER to look for the translation elongation factor (TEF) 1 alpha gene within a full genome assembly file. Commands used within this video: (NOTE THAT ANGLED BRACKETS ARE NOT ALLOWED IN THE DESCRITPTION SO I HAVE REPLACED THEM WITH "ANGLED BRACKET") #Make a MSA: /nfs1/BPP/LeBoldus_Lab/user_folders/mcmurtrs/bin/bin/mafft TEF1_copy.fasta ANGLED BRACKET TEF1_aligned.msa ...
How to install MUSCLE as part of the HMMER bioinformatics tool on linux operating system. Video #2
Переглядів 266Рік тому
MUSCLE is used to create multi sequence alignment files that can be used along with your full genome sequence to locate a gene or protein of interest. Video #1: How to install HMMER: ua-cam.com/video/eXYlTqT9rYE/v-deo.html Video #2: How to install bioinformatics program MUSCLE: ua-cam.com/video/XvZhhQgabf8/v-deo.html Video #2.2: How to find and download gene sequences from NCBI and Uniprot ua-c...
How to install the HMMER bioinformatics tool on linux operating system. Video #1
Переглядів 1,1 тис.Рік тому
Video #2: ua-cam.com/video/XvZhhQgabf8/v-deo.html Installing HMMER version 3.3.2. HMMER searches through full genome sequences for DNA sequence matches based on Hidden Markov Models constructed from sets of similar DNA sequences. Here is the command that worked for me on the part that I got stuck on: build=x86_64-unknown-linux-gnu Video #2: How to install bioinformatics program MUSCLE: ua-cam.c...
BBSketch tutorial - How to make a BlobPlot to visualize contamination in a genome.
Переглядів 110Рік тому
BBSketch is part of the BBTools toolbox that was developed by the Joint Genome Institute and allows you to create graphs to view possible contamination within genome assemblies. BBtools webpage: jgi.doe.gov/data-and-tools/software-tools/bbtools/ Acknowledgments: I would like to thank Jeff Chang and Alexandra Weisberg for showing me how to do this. A special thanks also goes out to the Joint Gen...
BBTools Tutorial - Check Genome Assembly for Contaminants using BBTools
Переглядів 424Рік тому
BBtools is a suite of bioinformatics tools developed by the Joint Genome Institute. This video displays a way of using BBTools to check your genome assembly for contaminants. Link to BBTools webpage: jgi.doe.gov/data-and-tools/software-tools/bbtools/
Plotting BUSCO Results - Tutorial on how to plot BUSCO scores as a bar chart.
Переглядів 534Рік тому
This video is a bit outdated, but the same concepts apply for creating a Benchmarking Universal Single Copy Orthologs (BUSCO plot).
BUSCO Tutorial - How to do a basic run with BUSCO to assess completeness of genomes.
Переглядів 2 тис.Рік тому
Benchmarking Universal Single-Copy Orthologs (BUSCO) is a very useful and commonly used tool in bioinformatics. It was developed by some really smart people and is useful for assessing the completeness of genome assembly, gene sets, and transcriptomes. Here is how you to do a basic run using this tool!
Assessing Genome Quality by Generating Assembly Stats with QUAST
Переглядів 1,3 тис.Рік тому
Quality Assessment Tool for Genome Assemblies (QUAST) is a useful tool for generating different summary assembly statistics of genomes. Here is a brief video showing how I have used it in the past. Please like and subscribe if you find these videos helpful and leave a comment if there are any related videos that you have found helpful. Thanks!!
How to install BUSCO on linux using wget command.
Переглядів 319Рік тому
This video quickly goes through installation of BUSCO on a linux operating system. Feel free to comment with any suggestions for other videos you would like to see. Thank you Usama Manzoor for suggesting this video be created. Link for video showing how to make a phylogenomic tree using BUSCO genes: ua-cam.com/video/gilA49YwSM4/v-deo.html
Example Run - Forest Vegetation Simulation (FVS) and Western Root Disease Model (WRDM)
Переглядів 6262 роки тому
CORRECTION: I realized after watching this that for the WRDM run I set the "Total Stand Area (acres)" and the "Total Root Disease Area (acres)" parameters wrong for a 1/10 acre fixed radius plot. The .25 and .625 are for a 1/20 of an acre fixed radius plot. For a 1/10 of an acre plot with 5 plots these values would be .5 and .125. Sorry about that! I am switching back and forth between two diff...
Creating a RAxML phylogenetic tree using BUSCO genes. Final video Video #5.
Переглядів 5312 роки тому
This video briefly goes through the final steps that you can use to create a RAxML maximum likely hood phylogenetic tree that will be ready for publication. Feel free to reach out if you have any comments, feedback, or questions. My email is mcmurtrs@gmail.com. Also be sure to check out the next tutorial found below on how to make the RAxML tree. Making an RAxML bootstrapped phylogenetic tree t...
Concatenate fasta files together for Phylogenetic tree made with BUSCO genes: Video 4
Переглядів 6252 роки тому
Video 1: ua-cam.com/video/gilA49YwSM4/v-deo.html Video 2: ua-cam.com/video/6KDvI74Ogzw/v-deo.html Video 3: ua-cam.com/video/ikEE6GGw0_0/v-deo.html Video 4 (current video): ua-cam.com/video/pyMmFCCj1QA/v-deo.html Video 5, final video: ua-cam.com/video/eFb1MJUNGgg/v-deo.html github.com/mcmurtrs/Making-a-Phylogenetic-Tree-with-BUSCO-Genes/blob/main/README.md Please like and subscribe if you found ...
Evolutionary analysis using a Phylogenetic tree made with BUSCO genes: Video 3
Переглядів 1242 роки тому
Evolutionary analysis using a Phylogenetic tree made with BUSCO genes: Video 3
Making a Phylogenetic Tree with BUSCO Genes: Video #2
Переглядів 3612 роки тому
Making a Phylogenetic Tree with BUSCO Genes: Video #2
Making a Phylogenetic Tree with BUSCO Genes: Video #1
Переглядів 6602 роки тому
Making a Phylogenetic Tree with BUSCO Genes: Video #1
Forest Vegetation Simulator won't open - Fix for Windows 10
Переглядів 1033 роки тому
Forest Vegetation Simulator won't open - Fix for Windows 10
Convert a VCF file into a data.frame for clustering algorithms in R
Переглядів 3,7 тис.3 роки тому
Convert a VCF file into a data.frame for clustering algorithms in R
Forest Vegetation Simulator (FVS) - Uploading new data sheet into simulator
Переглядів 1,2 тис.3 роки тому
Forest Vegetation Simulator (FVS) - Uploading new data sheet into simulator
Creating a Plot in R on the Cluster - CGRB - OSU - Video 2
Переглядів 203 роки тому
Creating a Plot in R on the Cluster - CGRB - OSU - Video 2
Using R on the Cluster - CGRB - Oregon State University - Video 1
Переглядів 443 роки тому
Using R on the Cluster - CGRB - Oregon State University - Video 1
Forest Vegetation Simulator (FVS) - Tutorial
Переглядів 2,8 тис.3 роки тому
Forest Vegetation Simulator (FVS) - Tutorial
5 Classes of Echinoderms with Brief Explanation of Example Species
Переглядів 1695 років тому
5 Classes of Echinoderms with Brief Explanation of Example Species
7 Characteristics Shared by All Living Things Biologoy
Переглядів 505 років тому
7 Characteristics Shared by All Living Things Biologoy
lol at the cat in the background
every one of those links are dead.
11567 Harry Knolls
Watsica Path
Holden Dale
42625 Rosenbaum Points
Hi I‘m a PhD student in molbio and have to teach myself a lot of bioinformatics and videos like yours help me a lot. Thanks
Hello i am also working on insect taxonomy. You have any lecture regarding nuclear genome study pf insect for phylogeny
Currently learning this, thank you!
Thank you very much. It was really useful. Greetings from Mexico!
thats me when guests come home
where are the attachments ???
Hi, thanks for the video! I am working with 332 genomes. So after I run BUSCO, I got 332 "full_table.tsv" files. I was wondering if there is a script to rename at once each "full_table.tsv" file into a specific "SAMPLEID_full_table.tsv". Thanks in advance
Thank you for the video. What file should be depend on ..contigs or scaffold?? And what is the corrected folder? Where or how should we use it?
You're welcome! Thanks for watching! If you are working with full genomes you will want to use the scaffolds file. The output statistics will be in the report.pdf file that is created after Quast finishes running.
does this install all of its dependencies?
I don't think that it does but I am not sure. If you are getting errors then you could try installing BLAST, HMMER, and Augustus first.
this was really helpful!!! thank you! Is it possible for you to make another video on how to interpret these results?
Wonderful 👑. #1 subs provider -> P R O M O S M.
Thanks dear. Waiting for next one
You are amazing
Thanks
Hey brother. Kindly share your email address.
shawnmcmurtrey@gmail
jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf (fo we need to write this command in the same way). when i am writing the job killed
github.com/gmarcais/Jellyfish/tree/master/doc
Can you please make a vidoe on kmer genie installation and use to KmerGenie estimates the best k-mer length for genome de novo assembly.
Thanks alot for all your efforts and time
The most important part in genome assembly we missed
Thanks
She is brilliant
Nice strategy
Cute one
Please make a video on kmergenie how to estimate the good kmer for genome assembly
You are doing really great
Very informative
Thank you
its really amazing and helpful
thankyou so much
yours all videos are very impressive and easy to understand
quast is good tool to check the assembly statistics. with BUSCO we can assess if the genome is repetitive through the number of duplicated BUSCO sequence. Ideally, all BUSCO genes should only have 1 gene count in the genome. thats why nowadays BUSCO is very useful tool. a kind request to please make a video on this as well
ua-cam.com/video/KtH1f5NrTvU/v-deo.html
For plotting BUSCO results on a bar graph: ua-cam.com/video/7_64uwXvcUk/v-deo.html
@@shawnmcmurtrey8090 thanks
Very informative.. thank you Can you do it using busco?
ua-cam.com/video/KtH1f5NrTvU/v-deo.html You are in luck my friend. I happened to have several tutorial videos that I made some time ago that I never got around to publishing them on UA-cam. You have inspired me to publish them on UA-cam!
Haha, thank you my friend. You have a good collection. You should upload it. Will be beneficial for many people around. Also u should continue this work. Best of luck 🙂❤️
@@usamadon2981 Thank you Usama! Best of luck to you as well.
Hey. Hope you are doing good. It would be really helpful if you can upload a video regarding the installation of BUSCO and also assessing genome quality of a sequence.
Here you go!! ua-cam.com/video/3mKhUPscFKw/v-deo.html Thank you for the suggestion Usama! Please like and subscribe if you found this helpful =)
@@shawnmcmurtrey8090 yes thank you 😊. Liked and subscribed. :) If you can get on to the second part of my comment about accessing genome quality of sequence of any organism. That would also be very helpful. Thanks in advance
@@shawnmcmurtrey8090 thank you so much. this is great
@@usamadon2981 Thank you for subscribing! QUAST is a useful tool that I have used in the past. ua-cam.com/video/t53D9AVj0I4/v-deo.html I will try to upload some more videos within the next day or two related to this subject.
Also add a video on phylogenetic analysis using R.. ggtree
not clear.
Thank you for these great videos! I am a grad student at SUNY ESF and they are very helpful!
Thanks for the video, it helped me a lot! :)
How do you use FVS in your Chrome Browser?
You can download it from the website here: www.fs.fed.us/fvs/software/complete.php If you are having trouble opening it after that there is also this video that might be helpful: ua-cam.com/video/bzQMynWD8ec/v-deo.html
Thank you so much this was very helpful!
I thought you would have to use Microsoft Access to enter data into FVS. We’re you able to upload your data using excel?
Hi Alex, I'm so sorry for the late reply. I somehow missed this comment. You can convert your excel spreadsheet into a Microsoft Access database with the website found here: forest.moscowfsl.wsu.edu/FVSDataConvert/
You can use excel files now too, the FVS program handles the converson to sql by itself
Have you by chance found a list of descriptions of the variables in the database spreadsheet?
Hey 26Rogue, sorry for the late reply. Are you referring to the variables in the first spreadsheet? The one titled "FVS_GroupAddFilesAndKeywords"?
@@shawnmcmurtrey8090 No, but I've figured it out. Just spending more time in the program, but thanks for checking back!
Thanks for sharing. Are you still learning FVS?
For sure, no problem! Yes, I am still learning the simulator and using it within my research. Do you use it often?
@@shawnmcmurtrey9571 I’m just trying to learn it myself. Caught some fine points in your video that I haven’t seen described anywhere else. In particular where plot size and stand acreage gets entered. So, very helpful.
I am starting to learn it right noe myself for an internship and a PAI estimate
yes
I've been fighting with my FVS template for hours!!! This helped me clear things up! Thank you!!!
I'm so glad that you found it helpful!! I will be posting more videos as I figure out the simulator more =)