Hello, I am from South Korea, and I appreciate all of your lectures, which are quite helpful. Can you kindly make a short video soon for R language beginners like me? How to install R software and packages, and if, the error shows during package installation, then how to solve them. Thank you so much.
Just a hint: It is recommended to use the --split-3 option instead of the --split-files. It deals with reads that do not have a mate and writes them to a third file.
Hi! Loved the lecture! Very concise and informative in a short period of time. Although, I have been facing one trouble. I have not been able to run vdb-config when I use the command ./vdb-config -i because my MacOS says , " vdb-config.3.0.5” cannot be opened because the developer cannot be verified." How do I resolve this issue so that I can successfully run the sra -toolkit across the SRR accession IDs?
This may be too late to help, but this is how i fixed the issue. What I did first was to change the permissions on vdb-config.3.0.10 by using the following command: chmod 755 vdb-config.3.0.10 in the terminal. If your mac is still giving you a privacy error, then go to system settings>privacy & security and scroll all the way down to find the security section. You should see the name of the file and give it permission from the system settings to run. It should run the next time. I hope this helps.
Was able to solve this issue with the following way: 1. try to follow along the tutorial, you will run in into the issue you are describing. 2. Open Settings>Privacy & Security. Scroll down. 3. Find the section under 'Security', where you will see an option for 'Open vbd-config.3.1.0 anyway', there is thould ask you for your password or fingerprint and start to work, next time you type up the command in terminal ;) i know this is mad late, but i hope it helps!
Hi there. Thank you for the nice tutorial. Just wanted to ask: 1. is there a way to select a target folder where the fastq files will be download directly? because by default they are downloaded to home directory 2. can we download the files in compressed form (.gz format)? Thank you.
Hi, great video. Quick question: can the SRA toolkit downloaded fastq data be directly used for STAR alignment? Will the file name and header cause any errors? thanks!
thanks! But I am still puzzled on the point of how many sra files one should download. So lets say i want to benchmark tools on heart tissue for tabula muris. Do i have to download every .sra file which is almost 2 Terrabyte? Is there no information about cell types in the organ/tissue ?
Hi. First of all. I would like to congratulate you because all the content you are disseminating is very helpful :). Regarding the video, I have a few questions. As you know, it is possible to find multiple runs (SRR id) for one experiment (SRX). I would like to ask you what to do when this occurs. I have read when multiple SRR are found within an SRX entry, runs should be concatenated to finally produce 1 SRR run per SRX entry. Is that correct? Best regards, Felipe
Each SRR is a separate sample/replicate. You should not merge SRR IDs into one. One experiment (SRX) can have multiple samples and/or replicates and hence multiple SRRs.
Thank you! Everything worked for me- but I have almost 3000 SRR ID's that need to be downloaded. In this case, do you know what command I need to use to get the entire file downloaded instead of just one individual?
For me, I get this error message saying that vdb-config.3.1.1 cannot be opened because apple cannot check if it is malicious and makes me kill the operation
Thank you for your video! When I run ./vdb-config -i I got this error “vdb-config.3.0.0” cannot be opened because the developer cannot be verified. Would you please tell me how to fix this?
@@nayeemanushrat3174 The error is telling you that it cannot find the executable fasterq-dump. Can you send me a screenshot of the output of ls() where you are trying to run this command, on my email?
Not necessarily, it can be used in other OS systems as well (github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit). However linux is preferred and if often hassle free,
Hi! There's a query As you explained meaning of all prefixes used in accession numbers ,in continuation of this i want to know what is the meaning of prefix ERX...
hank you for your video ! When I run ./vdb-config -i I got this error “vdb-config.3.0.0” cannot be opened because the developer cannot be verified. Would you please tell me how to fix this?
This version of the SRA toolkit does not contain the command to prefetch we are now on version 3.0.0 and this is version 2.1.1 it is not useful anymore. The tutorial needs to be updated.
Thanks for pointing it out! There are two ways to download Runs - using prefetch or using fasterq-dump (www.ncbi.nlm.nih.gov/sra/docs/sradownload/). If you prefer to download Runs using the former method, you should use the newer version. Having said that, there will be more updates in the future for SRA toolkit (like every bioinformatics tool). The idea behind this tutorial is to demonstrate how one can use an existing package to download sequencing runs from NCBI. It is common practice among bioinformaticians to make sure they are using the updated/alternate functions that come along with these newer versions.
Thank you so much! This tutorial is very easy to understand for me. And very usefull for beginner.
Thank you so much for such a thorough video, well done! :)
Hello ! Thank you for this useful material!! Could I please squeeze in to ask why did my Bash returned "Segmentation Fault"? Thank you so much!
Amazing channel! Thank you! You are helping me a lot with my dissertation 🎉
Hello, I am from South Korea, and I appreciate all of your lectures, which are quite helpful. Can you kindly make a short video soon for R language beginners like me? How to install R software and packages, and if, the error shows during package installation, then how to solve them. Thank you so much.
I will surely consider making a video covering basics of R and installing packages in R :)
Your videos are saving my thesis ty so much!
Just a hint: It is recommended to use the --split-3 option instead of the --split-files. It deals with reads that do not have a mate and writes them to a third file.
Bohat vadia video banaya hai aap ne!
Thank you so much for such a great explaination! 😁
Didi please upload more videos on rna seq data analysis
why have thy made SRA download so complicated? It should be simple, why all the hassle? why one has to go thru the terminal?
really useful
Hi! Loved the lecture! Very concise and informative in a short period of time. Although, I have been facing one trouble. I have not been able to run vdb-config when I use the command ./vdb-config -i because my MacOS says , " vdb-config.3.0.5” cannot be opened because the developer cannot be verified."
How do I resolve this issue so that I can successfully run the sra -toolkit across the SRR accession IDs?
This may be too late to help, but this is how i fixed the issue. What I did first was to change the permissions on vdb-config.3.0.10 by using the following command: chmod 755 vdb-config.3.0.10 in the terminal. If your mac is still giving you a privacy error, then go to system settings>privacy & security and scroll all the way down to find the security section. You should see the name of the file and give it permission from the system settings to run. It should run the next time. I hope this helps.
Was able to solve this issue with the following way:
1. try to follow along the tutorial, you will run in into the issue you are describing.
2. Open Settings>Privacy & Security. Scroll down.
3. Find the section under 'Security', where you will see an option for 'Open vbd-config.3.1.0 anyway', there is thould ask you for your password or fingerprint and start to work, next time you type up the command in terminal ;)
i know this is mad late, but i hope it helps!
Hi there. Thank you for the nice tutorial. Just wanted to ask:
1. is there a way to select a target folder where the fastq files will be download directly? because by default they are downloaded to home directory
2. can we download the files in compressed form (.gz format)?
Thank you.
Thank you so much for this tutorial!
Hi, great video. Quick question: can the SRA toolkit downloaded fastq data be directly used for STAR alignment? Will the file name and header cause any errors? thanks!
AFTER DOING ALL LIKE YOU SAID, WHEN I DO FINAL STEP FOR DOWNLOAD ITS SHOW SYSTEM COULD NOT FIND PATH
PLEASE HELP ME
really helpful video. Such useful and amazing content.
thanks! But I am still puzzled on the point of how many sra files one should download. So lets say i want to benchmark tools on heart tissue for tabula muris. Do i have to download every .sra file which is almost 2 Terrabyte? Is there no information about cell types in the organ/tissue ?
Nice explanation madam, how this sra data useful madam
Hi. First of all. I would like to congratulate you because all the content you are disseminating is very helpful :).
Regarding the video, I have a few questions.
As you know, it is possible to find multiple runs (SRR id) for one experiment (SRX).
I would like to ask you what to do when this occurs. I have read when multiple SRR are found within an SRX entry, runs should be concatenated to finally produce 1 SRR run per SRX entry. Is that correct?
Best regards,
Felipe
Each SRR is a separate sample/replicate. You should not merge SRR IDs into one. One experiment (SRX) can have multiple samples and/or replicates and hence multiple SRRs.
Great video, thank you! I hope you can make a tutorial on how to batch download sequences from SRA.
Sure, I will make a video on it. Thanks for the suggestion.
@@Bioinformagician hi, is there a video on how to batch download sequences from SRA? i dont see it on your channel?
Thank you for this video !!
Thank you! Everything worked for me- but I have almost 3000 SRR ID's that need to be downloaded. In this case, do you know what command I need to use to get the entire file downloaded instead of just one individual?
I'm also looking for a way to so this. Did you find a solution?
@@julkajulka6751 Hey could you figure this out? I am also looking for the same
How many time it takes for download single sra file at M1 pro?
For me, I get this error message saying that vdb-config.3.1.1 cannot be opened because apple cannot check if it is malicious and makes me kill the operation
allow it in your mac pravacy and security settings and run it again
write this on terminal : "sudo spctl --master-disable" and disable the gatekeeper of mac then enable it by writing: "sudo spctl --master-enable"
So, what's the next step using the same data we downloaded. How to merge this two fastq files for mapping to to references ?
👍may I know how to check the download result if my broadband connection is not very stable? Thx
Nice video, Can you show us how to make it with an accession list? Thanks.
You could loop through each line in your accession list file in bash. It shouldn't be difficult.
@@Bioinformagician Is it possible to download all data in the accession list at the same time?
Thank you for your video! When I run ./vdb-config -i I got this error “vdb-config.3.0.0” cannot be opened because the developer cannot be verified. Would you please tell me how to fix this?
Hİ!
I take same error. Did you solve this ?
@@recepuyar6423 I remember go to setting and allow system to run this software.
Fasterq-dump --split-files command not found. What should I do?
Are you running this command within the bin/ folder or sra-toolkit?
@@Bioinformagician Fasterq-dump --split-files command not working, kindly help please
@@nayeemanushrat3174 Are you running this command within the bin/ folder or sra-toolkit?
@@Bioinformagician I ran this exactly you showed in the video, still not working 😮💨
@@nayeemanushrat3174 The error is telling you that it cannot find the executable fasterq-dump.
Can you send me a screenshot of the output of ls() where you are trying to run this command, on my email?
How do we get GSE Id and can i download SRA tool kit in my phone ?
Hello, thank you for providing this video. I just wonder if I need to make a linux environment to excute SRA toolkit.
Not necessarily, it can be used in other OS systems as well (github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit). However linux is preferred and if often hassle free,
hello, pl prepare video of metadata file prepare in R for gene expression analysis.
Hi!
There's a query
As you explained meaning of all prefixes used in accession numbers ,in continuation of this i want to know what is the meaning of prefix ERX...
Check this out - www.ncbi.nlm.nih.gov/sra/docs/srasearch/
I am still not sure how to find the latest uploaded data on SRA….
This split file command is only for paired end sequence?
Yes, for single ended reads, we don't use --split-files option
@@Bioinformagician thanks
hank you for your video ! When I run ./vdb-config -i I got this error “vdb-config.3.0.0” cannot be opened because the developer cannot be verified. Would you please tell me how to fix this?
Go to System settings, Privacy and Security, there will be a pop-up asking for permission to open the file!
thank you🙂
yo sister can you make a video on raw data processing after we download from ncbi??????
I need to split 20 files in windows , could u please help me with commands
my location of public cache is blank ...kindly help on this
Thank you
This version of the SRA toolkit does not contain the command to prefetch we are now on version 3.0.0 and this is version 2.1.1 it is not useful anymore. The tutorial needs to be updated.
Thanks for pointing it out! There are two ways to download Runs - using prefetch or using fasterq-dump (www.ncbi.nlm.nih.gov/sra/docs/sradownload/). If you prefer to download Runs using the former method, you should use the newer version.
Having said that, there will be more updates in the future for SRA toolkit (like every bioinformatics tool). The idea behind this tutorial is to demonstrate how one can use an existing package to download sequencing runs from NCBI. It is common practice among bioinformaticians to make sure they are using the updated/alternate functions that come along with these newer versions.
It will more better if the directors voice a little bit increased
I shall take that into consideration next time. Thanks!
Should have shown how to add the folder to path permanently.
why don't they just give you the "download as" window, and then you click "download to folder downloads"
Please can we have call, I am struggling in ngs cancer profiling project