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03 What is the FASTQ format? (Download files from NCBI's SRA)
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- เผยแพร่เมื่อ 28 ก.ย. 2016
- This video is part of a video series by www.nextgenerationsequencinghq.... It introduces the basic work flow of how to get information from your next generation sequencing data.
This video explains how to download published data stored in ncbi's sequence read archive (SRA). You can download sample files to practice data analysis on. You will further learn what the FASTQ format is.
Thank you, it helped me a lot, your presentation also precise and informative
Thank you very much for the course.
it was perfect thank you.I also have a question, what is the difference between getting the fastq files from the ftp at the bottom of a serie in GEO and getting them from SRA which takes us to the page of sequences with GSM files?
Thank you bro well explained I'm from India, Post more videos about NGS analysis
thank you sir~! this is very useful vid for me ~!
Hello, thank you for your great tutorials, I am not getting along with this Ubuntu, it is slow specially if I open the web browser , I can't manage to use the usual shortcuts of the keyboard (such as copy and paste), I am using iMAC, could you give me any advice concerning that? thank you so much
Thank you very much for the course. At 5:17 an error has showed up in your terminal and at 5:18 the error was resolved. Kindly let us know how you resolved the error.
Hi, thanks for your video. Which terminal do you use? Mine is Windows Prompt or Anaconda prompt and they don´t recognize those commands. Sorry, I don´t have so much experience with this: I am able to download the databases for the bioproject "PRJNA406998", but I cannot see the information on it. Thanks.
The following message appears when I click on the above link:
"No information is available for this page".
Would you please share your link!
Hi, may I know that we could run the analysis through the Oracle VM in the laptop without using the huge storage in the PC? Last time I tried using my own laptop to run the fastq file through the Oracle, but it was not succeeded.
hi everything seems installed correctly but then i type the prefetch command as you write and the result is: "/usr/bin/prefetch: cannot execute binary file: Exec format error"
I cannot download the file with command. it shows this file does not exist. Could you help? thanks
I am unable to download the SRA file .. can you give some suggestions
Generally, SRA file is large, like more than 4 or 5 GB so sometimes our network get disconnected in between, what will happen, can we know even how much have been downloaded?
Hi all, how can you use ctrl+c, ctrl +v , on your virtual machine? It does not allow me
what do to when [sudo] password for sequencing: appears? it doesnt proceed. I pressed enter and it said Sorry try again
Hi, I run the sudo apt-get install sea-toolkit command and I get the error “Package ‘sar-toolkit’ has no installation candidate” can you help me?
hi, have you fixed the problem?
@@wenziren9129 hi did you solve it?
I encountered a problem like this..
E: Unable to locate package sra-toolkit
if anyone gets an error E: unable to locate package, try updating using: 'sudo apt-get update' and try try the SRA-toolkit download again. May not work for you, but worked for me.
Thank you!!!
thanks
Hi Thanks for this tutorial. Everything till 6:04 is clear, however when i am downloading the cart file by pasting the SRR number.... I get the same message as earlier... 'SRR2079547' cannot be found! How did you manage to download?
Hi Shangjun, Could you please explain what you did with a bit more detail. I am new to ubuntu so will appreciate some help.
Hi Pallavi, did you manage to get around the downloading problem then. Could you share your solution
thanks
Bilal
never mind guys I figured what Shangjun meant and it worked.
cd sratoolkit.2.8.2-1-ubuntu64/bin$ ./prefetch SRR2079547
you should install the sra-toolkit from the github.com, following the exact install step.(I have the same problem and have solved it)
thx
Use grep to search for @ and you get the number of sequences rather than dividing by 4 which is clumsy
it didn't work, because @ is present in between many sequences. So I used "SRR" or "length" dividing by 2
Cool website
The following message appears when I click on the above link:
"No information is available for this page".
Would you please share your link!
there is error showing during srr file downloading
Why did you take SRA website if you wanted to download using Ubuntu? It's so confusing. Explain one method first and then go to the other one.
Hi， Thanks a lot! when I followed your video, I found a problem, mentioned like this "Maximum file size download limit is 20,971,520KB
2018-10-30T20:59:18 prefetch.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR2079547' - Obsolete software. See github.com/ncbi/sra-tools/wiki ( 406 )
Redirected!!!
2018-10-30T20:59:18 prefetch.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2018-10-30T20:59:18 prefetch.2.3.5 err: path not found while resolving tree within virtual file system module - 'SRR2079547' cannot be found.
" .
Hello, how did you managed this problem?
Same error. Please somebody help.