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How do I Creat count table from raw seqdata ( fastq) and run Deseq2?

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

deseq2 count table
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updated by ATpoint ATpoint • written by jaqx008 jaqx008

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!

• 1 views • link
written by GenoMax GenoMax

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.

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written by WouterDeCoster WouterDeCoster

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

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written by jaqx008 jaqx008

3 answers

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.

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written by Matteo Schiavinato Matteo Schiavinato

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

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written by jaqx008 jaqx008

Full tutorial here and here.

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written by ATpoint ATpoint

Please check DESeq2 vignette or RNASeqGene workflow.

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written by GenoMax GenoMax

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