Analyzing Public Datasets 2: Finding the Data

In this new series, we'll learn how to access and analyze public datasets resulting from next-generation sequencing techniques such as Illumina and 454.

This video shows how to find a sample dataset, upload it to Galaxy, and process it for alignment.

[maximilianUTU]

Congratulations!!
This is how a videotutorial should be:
step-by-step (meaning really microstep by microstep),
everything slowly explained even for old idiots
(like me) to comprehend, and nothing that does not
belong straight to the subject.
Plus a clear, modulated voice,  good audio, good
video (readable) - man, You are my hero!!
I have seen somany poor videotuts - even from
big companies with big video marketing budgets. 

[codestorywithMIK]

When i tried to upload the fastq file(>10 GB), it showed this error:
Failed: File exceeds 2GB. Please use a FTP client.
I don't know how to use FTP client and what does that Failed statement mean ? Can somebody please explain ?

[Maxbario]

Arturgreensward, I am just newbie in this sort of genome analysis... So when I started to follow your video I found that supplementary data are not longer available in fastq.txt format, instead it's presented in .sra format which confuses me.

[frederichleclerk]

Hi, I'm looking this fantastic tutorial now, 8 years later and the file you use is not avaible, instead there is a file called in TAR format which i don't know what it means. How I should preceed to do the analysis with this file? Because it is 2'6 Gb

[chicong]

Hello, when I drag the fastq file to terminal it denied to open it, how can I run the file by terminal like you? Thank you

[Maxbario]

Thank you very much for your response. Actually I have found out where to download this toolkit, but unfortunately, my terminal doesn't know how to convert this .sra format to fastq with fastq-dump command. I am just following all steps of NCBI tutorial. Would it be possible for you to make a video tutorial about this? Thanks for you help!

[bernardobello_PhD]

Hey David! Can I switch off the computer when FASTQ groomer files are being created by Galaxy.

Thank you and good job!

[yona]

Hey David! Just a quick question. You used "less" in your terminal to view the file; do you know the command to do that for command prompt in pc?? Thanks in advance! :)

[khana]

Hi, when I tried to use the ftp to download the fastq data, files such as SRR034580.sra data showed up. No fastq.bz2 data. What am I doing wrong? Thank you,

[Arturgreensward]

No, but if you're doing some kind of Unix shell on the PC then "less" should work there as well.

[Arturgreensward]

Nothing wrong but you'll need to convert your data from SRA to fastq. You'll need to use the SRA toolkit that NCBI provides. Just do a Google search for "SRA toolkit NCBI".

[Arturgreensward]

All the processing happens on Galaxy so you should be fine.