0
$\begingroup$

I am trying to understand expression of a certain protein across Pseudomonas species. I downloaded an SRA file from NCBI and converted it to a fastaq file. I am not able to understand how to interpret and analyse this file. I want to get the mRNA sequence and see which genes are being expressed and find the mRNA of interest.

How do I proceed with getting the mRNA sequences and then for mapping them to genome?

$\endgroup$
1
  • $\begingroup$ For some studies, in GEO they also include the processed counts. You can also see whether it's the case for your study $\endgroup$
    – StupidWolf
    May 12, 2020 at 14:54

1 Answer 1

1
$\begingroup$

SRA files are raw sequencing data that have been converted to the NCBI storage format. These can be converted to fastq files, e.g. with fastq-dump from the SRAtoolkit.

Beyond that I suggest you start with the Hitchhiker's GUide to RNA-seq and the DESeq2 workflow to get a background. Be sure to extensively browse the web for vignettes, guides and tutorials. YOu will find helpful resources to get started.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.