Question: Gene expession in RNA-seq data from SRA
gravatar for ingus55
6 days ago by
ingus550 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!

ADD COMMENTlink modified 1 day ago by Jennifer Hillman Jackson25k • written 6 days ago by ingus550
gravatar for Jennifer Hillman Jackson
1 day ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see the Galaxy Tutorials for RNA-seq analysis examples and workflows:

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 COMMENTlink written 1 day ago by Jennifer Hillman Jackson25k
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