Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Gene expession in RNA-seq data from SRA
0
gravatar for ingus55
6 days ago by
ingus55 • 0
Germany/Kiel/Uni
ingus55 • 0 wrote:

Hi! I would like to check the expression of my gene of interest in expression data loaded fro SRA. It should be induced comparing activated vs non activated cells. At this stage it would be enough to visualize on the genome browser the signals of the mapped reads in the two different conditions. I have used Bowtie2 to map the reads and visualize them on the UCSC browser. It seems to work, but my questions are: 1) am I missing some steps, before the mapping? 2) do I have to run Cutadapt first? 3) do the data have to be normalized somehow in order to be able to compare the tow conditions?

Thanks a lot for the help!
rna-seq alignment bowtie hisat2 • 32 views
ADD COMMENT • link •
modified 1 day ago by Jennifer Hillman Jackson ♦ 25k • written 6 days ago by ingus55 • 0
0
gravatar for Jennifer Hillman Jackson
1 day ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please see the Galaxy Tutorials for RNA-seq analysis examples and workflows: https://galaxyproject.org/learn/

Start here. Bowtie is fine for mapping DNA or unspliced RNA. But for most use cases, HISAT2 is a better choice for mapping spliced RNA.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 1 day ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour