Question: Does re-sequencing fastq files contain DNA or RNA sequences?
gravatar for mohammedtleis
14 months ago by
mohammedtleis0 wrote:

Dear Biostar members,

I have a very basic question about some fastq files I got. All what I know is that they are re-sequencing fastq files. My question is whether they are actually DNA or RNA sequences? In general, Is there a way to tell by looking into the contents? Does it matter to know this? and when we talk about hg19 or hg38 human genomes, are these merely DNA sequences?

My aim is to compare these files with a reference genome. So after I get an answer to this basic question. I will start researching on how to do the comparison using galaxy. For instance I have no idea whether I will have to compare these to the full genome or to a predefined chromosome locations. After that I would like to learn what processes and tools I need to use to achieve this goal. For example do I need to index? align? assemble reads?

So any tips that would help in understanding the issue is very much appreciated.

Best Regards, M. Tleis

rna-seq galaxy • 336 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by mohammedtleis0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


First, check with the lab that produced the data to find out of the sequence data represents DNA or RNA - it makes a big difference in how downstream analysis is done. You also need to know what type of data is represented. RNA-seq, some form of ChIP-seq, or other.

The reference genome itself always represents DNA, however, RNA data is often (but not always) aligned to the genome using alignment tools that produce spliced alignments.

Tutorials that explain and have example protocols for analyzing data can be found here:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson25k
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