Question: (Closed) How do I Creat count table from raw seqdata ( fastq) and run Deseq2?
0
gravatar for jaqx008
10 weeks ago by
jaqx00840
jaqx00840 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 • 141 views
ADD COMMENTlink modified 10 weeks ago by ATpoint15k • written 10 weeks ago by jaqx00840

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 10 weeks ago • written 10 weeks ago by genomax65k

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 10 weeks ago by WouterDeCoster38k

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

ADD REPLYlink written 10 weeks ago by jaqx00840
2
gravatar for Macspider
10 weeks ago by
Macspider2.8k
Vienna - BOKU
Macspider2.8k 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 10 weeks ago by Macspider2.8k

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

ADD REPLYlink written 10 weeks ago by jaqx00840

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 10 weeks ago by genomax65k
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gravatar for ATpoint
10 weeks ago by
ATpoint15k
Germany
ATpoint15k wrote:

Full tutorial here and here.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by ATpoint15k
0
gravatar for genomax
10 weeks ago by
genomax65k
United States
genomax65k wrote:

Please check DESeq2 vignette or RNASeqGene workflow.

ADD COMMENTlink written 10 weeks ago by genomax65k
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