How to examine/validate my result of read-count from HTseq-count

Question

[Pei]

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!

Answer 1

[Malachi Griffith]

You may find some useful exercises and related concepts at http://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.

[Pei]

Thanks a lot!