text: user8767: 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?
  
  user-1: 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.
  
original_text: 8767: <p>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.</p>
  
  <p>How do I proceed with getting the mRNA sequences and then for mapping them to genome?</p>
   -1: <p>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. </p>
  
  <p>Beyond that I suggest you start with the <a href="https://peerj.com/preprints/27283/" rel="nofollow noreferrer">Hitchhiker's GUide to RNA-seq</a> and the <a href="http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" rel="nofollow noreferrer">DESeq2 workflow</a> to get a background. Be sure to extensively browse the web for vignettes, guides and tutorials. YOu will find helpful resources to get started.</p>
  