Question: How to examine/validate my result of read-count from HTseq-count
gravatar for lin.pei26
3.5 years ago by
lin.pei2670 wrote:

Hi all:


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 ?


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 • 1.6k views
ADD COMMENTlink modified 3.5 years ago by Malachi Griffith17k • written 3.5 years ago by lin.pei2670
gravatar for Malachi Griffith
3.5 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

You may find some useful exercises and related concepts at

Table of contents:

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 3.5 years ago • written 3.5 years ago by Malachi Griffith17k

Thanks a lot!

ADD REPLYlink written 3.5 years ago by lin.pei2670
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