Bitesize Bioiniformatics: Downloading sequencing data from GEO and SRA
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- čas přidán 27. 06. 2024
- In this video we're going to go through some of the different options you have for downloading raw sequence data in fastq format from the big public sequencing databases, GEO and SRA. We'll look at a couple of different database interfaces and other accessory tools which can help unlock the valuable data that these systems provide.
Some of the sites and tools which we mention specifically are:
GEO: www.ncbi.nlm.nih.gov/geo/
ENA: www.ebi.ac.uk/ena
SRA Explorer: sra-explorer.info/
SRA Toolkit: ncbi.github.io/sra-tools/inst...
SRA Downloader: github.com/s-andrews/sradownl... - Věda a technologie
Thank you soooo much. . . . After cracking my head for 3 days . . For the raw sequence data. . Finally I understood. . . . Thanks to you
Thank you for all these amazing videos. They are highly recommend for biologist who lack bioinformatics skills. Can you please make videos on histone ChIP seq analysis starting from fastqc to GO since all the available ones are really old. Thanks again and please keep up the great work 👍
This is an excellent video. It clarifies so much! Cheers!
Thanks, really helpful video. Keep them coming!
Very useful resource for us dummies. Thank you!
Great video and walk-through. Thank you!
This video is Amazing! Thanks for uploading it
Thanks. It's a great guide!
This was super useful! Thank you so much!!!
Thank you very much for this valuable content. Helped me a looooot
What a invaluable material
such a valuable content mashallah. thanks a lot.
Thank you for your quick response...
Please contact us at babraham.bioinformatics@babraham.ac.uk with any questions. Thanks.
Amazing video - I love the --cantspell :D
Thanks! Fortunately they've fixed that so it's not an issue with newer releases. We've also expanded support in SRAdownloader - it can now also download fastq files directly from ENA which seems quicker and more reliable, and it can also just be fed a list of SRR accessions (or a single SRR name) to get the corresponding data.
Very great lesson! I have a question, at around 15:02min, when you swich the downloaded fastq data to analysis screeen, what is that analysis app? I cannot get it at this step. Thank you very much!
Hi, the software download at 15:02 is the route (direct from NCBI) which is NOT recommended. Other options are detailed from 17:04
Thank you for the informative video. I have a question and would request you to help me out. Should we consider SRR files as technical replicates or should we have to pool the SRR files for further analysis?
If you have multiple SRR accessions for a single SRX then the implication from the strucutre of the database is that these are technical replicates of the same sample, so the same library split across multiple sequencing lanes. I would therefore look at merging them before analysing them. I'd also recommend reading the associated paper and metadata in case the submitters have done something strange within the constraints provided by GEO/SRA though.
@@simonandrews5604 Thank you so much for helping me out.
Great and informative video. Thanks for this. But is it possible to convert the downloaded data to say excel/csv format unaltered?
The raw data you get from these databases are not going to be suitable to put into something like excel - they'd be way too big. If you're after quantitations generated from the data then every entry in GEO has to have a quantitated data file with it. There are no fixed rules for what this file has to be so the contents vary wildly from sample to sample. In some cases you would have a file which would be compatible with a spreadsheet (a matrix of samples vs counts or normalised expression for example), but in many cases even this won't be suitable (bigWig files for whole genome quantitation for example). The quantitated data will appear as a supplementary file at the bottom of the sample's GEO page. The metadata on the sample will describe what the quantitation is and how it was generated.
A more reliable way to deal with this is to process the data to generate the quantitations you want. It's more work but at least you know what you're getting and you can do it consistently.
@@simonandrews5604 Thank you for your detailed clarification. I really appreciate it.
Thanks so much for this video. I am running Ubuntu 20.04 and can't get sradownloader installed on it. Does sradownloader work on Ubuntu 20.04?
It should do - anywhere with a recent python should work. If you're having problems can you open an issue in the sradownloader issue tracker and post the full output of the command you ran.
@@simonandrews5604 Thanks so much for the quick response. I will update my python and reinstall it. Once again thanks so much
Hmm "Bitesize" Bioinformatics...this video is 45m long...and goes well outside the scope of SRA.