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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?

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  • $\begingroup$ 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

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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.

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