Question: How to examine/validate my result of read-count from HTseq-count
0
gravatar for lin.pei26
3.8 years ago by
lin.pei2690
China
lin.pei2690 wrote:

Hi all:

QUESTION:

usually how do you check the read count results before moving on ? Any way to statistically assess the result or visualize the read count data ?

background

I have stranded and pair-end drosophila RNA-seq data.

after running htseq-count, I write my script to get the read counts for gene (not transcripts)

 

Thanks in advance!

 

rna-seq • 1.7k views
ADD COMMENTlink modified 3.8 years ago by Malachi Griffith17k • written 3.8 years ago by lin.pei2690
1
gravatar for Malachi Griffith
3.8 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

You may find some useful exercises and related concepts at www.rnaseq.wiki.

Table of contents:

https://github.com/griffithlab/rnaseq_tutorial/wiki

Module 3 covers use of Cufflinks and htseq-count. In particular refer to the expression section, followed by differential expression, and finally visualization and summarization of the results.  Several R scripts are linked from this last section that describe various approaches and packages for visualization of expression estimates. 

As one of the creators of this resource I'm biased, but I recommend that you work your way through the whole tutorial and read the companion paper as an introduction: Informatics for RNA-seq: A web resource for analysis on the cloud. The Supplementary Materials contains tables with: answers to common questions, tools for various RNA-seq applications, resources for RNA-seq analysis, and ways to obtain more didactic RNA-seq instruction.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Malachi Griffith17k

Thanks a lot!

ADD REPLYlink written 3.8 years ago by lin.pei2690
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1406 users visited in the last hour