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-   -   My NGS data. What to use: galaxy, R or ? (http://seqanswers.com/forums/showthread.php?t=89686)

KB* 06-08-2019 04:10 AM

My NGS data. What to use: galaxy, R or ?
 
Hi all,

Really hope for your help, guys.

I finally got my ChIP-Seq data back. Hoping it is not too bad. You can check for the history of my libraries prep here:

http://seqanswers.com/forums/showthread.php?t=88202

Now, I want to analyse the data by myself as much as I can. Unfortunately due to the cost, attending a workshop is out of question.. An online course, possibly. If you know one, please share with me.

The question is what would be the best approach to analyse my data? What do I need?

I know R and I was participating in assembling a genome "on cloud", but I do not remember much. For the best of my memory I will not be able to work with my data on my computer. I have 20 files (forward and reverse reads) about 3.5 Gb zipped.

I tried to load them on galaxy via FTP, but it is painfully slow (~24h each! file). Then, some files possibly got corrupted - FastQC in galaxy fails on them.

I found a couple of resources to read:
a list on aps on biostars:
https://www.biostars.org/p/272802/

Using Galaxy. A workshop from Abcam:
http://docs.abcam.com/pdf/webinars/a...is-webinar.pdf
and
https://www.youtube.com/watch?v=pJON0-e_I3o

ChIP data with Galaxy. From Galaxy:
https://galaxyproject.org/tutorials/chip/
and
https://galaxyproject.github.io/trai.../tutorial.html

Using R:
http://biocluster.ucr.edu/~rkaundal/...q/ChIPseq.html

It looks like uploading to galaxy will never finish. Does it make sense to try to do everything in R? What is the most common pipeline used for NGS data analysis.

If I will not be able to work with the files on my computer, does anybody know how to organise that "cloud commuting" in detail? I have Amazon cloud account and virtual box. What else and how?

Thank you!

frascom 06-10-2019 05:20 AM

It Should not take that long to FTP into Galaxy.

Try the Galaxy server https://usegalaxy.eu/ I think its great and good resources about how to upload data and analyse. I'm not sure if it has tools for ChipSeq but check it out.

You can also upload data straight from Dropbox on Galaxy too.

KB* 06-10-2019 05:59 AM

@frascom

Than you! I figured that up. I used institutional internet with wired access to the internet. And it was fast :)) wifi is much slower. In particular from a private (home) network.

I am now using galaxy.

Not quite sure how much to trim the data and whether the data is Ok by itself. I will post here FastQc reports. Hopefully I will find the answers.

Thank you very much again


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