Question: (Closed) How do I Creat count table from raw seqdata ( fastq) and run Deseq2?
0
gravatar for jaqx008
18 months ago by
jaqx00870
jaqx00870 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 • 631 views
ADD COMMENTlink modified 18 months ago by ATpoint36k • written 18 months ago by jaqx00870

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 18 months ago • written 18 months ago by genomax87k

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 18 months ago by WouterDeCoster44k

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

ADD REPLYlink written 18 months ago by jaqx00870
2
gravatar for Macspider
18 months ago by
Macspider3.1k
Vienna - BOKU
Macspider3.1k 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 18 months ago by Macspider3.1k

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

ADD REPLYlink written 18 months ago by jaqx00870

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 18 months ago by genomax87k
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gravatar for ATpoint
18 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

Full tutorial here and here.

ADD COMMENTlink modified 18 months ago • written 18 months ago by ATpoint36k
0
gravatar for genomax
18 months ago by
genomax87k
United States
genomax87k wrote:

Please check DESeq2 vignette or RNASeqGene workflow.

ADD COMMENTlink written 18 months ago by genomax87k
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