Question: (Closed) How do I Creat count table from raw seqdata ( fastq) and run Deseq2?
0
gravatar for jaqx008
7 months ago by
jaqx00850
jaqx00850 wrote:

Hey Guys, I am new to Deseq2. However, I want to generate a count table for my sample to be used in Deseq2. I have four replicates of treated and untreated files. Help. Thanks

count table deseq2 • 275 views
ADD COMMENTlink modified 7 months ago by ATpoint23k • written 7 months ago by jaqx00850

Hello jaqx008!

Plenty of resources included in comments/answers.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax71k

Help.

Try helping yourself before asking others. There are great tutorials available, and documentation. If you get stuck you are free to ask for help, but spend some effort first.

ADD REPLYlink written 7 months ago by WouterDeCoster41k

Actually I did tried but I guess I was confused. But thanks and I will look more next time

ADD REPLYlink written 7 months ago by jaqx00850
2
gravatar for Macspider
7 months ago by
Macspider2.9k
Vienna - BOKU
Macspider2.9k wrote:

Map your reads with your mapping software of choice (just needs to output a sam file) and then run that sam file through a feature counter, for example HTSeq.

ADD COMMENTlink written 7 months ago by Macspider2.9k

I see now. So do I do HTseq from a web interface or I have to install it?

ADD REPLYlink written 7 months ago by jaqx00850

You will need to use Galaxy to run HTseq if you need a GUI. DESeq2 can be used at https://yanli.shinyapps.io/DEApp/ via a GUI once you have counts.

ADD REPLYlink written 7 months ago by genomax71k
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gravatar for ATpoint
7 months ago by
ATpoint23k
Germany
ATpoint23k wrote:

Full tutorial here and here.

ADD COMMENTlink modified 7 months ago • written 7 months ago by ATpoint23k
0
gravatar for genomax
7 months ago by
genomax71k
United States
genomax71k wrote:

Please check DESeq2 vignette or RNASeqGene workflow.

ADD COMMENTlink written 7 months ago by genomax71k
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