I am planning to confirm the expression of my gene in a bacterial species based on RNA-seq data available in SRA. I am confused by how I should deal with it. Do I need to assemble the transcriptome first and then do blast search? Or is there any other way in which I can make sure that the gene is expressed without assembling the transcriptome? Thanks!
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It depends on what information is available for the species you are working on: best case there is a reference genome and good annotation (GTF, GFF file on UCSC, Ensembl). Then you can align against the reference and use the GTF/GFF to determine number of reads at a particular feature (gene, exon) of interest, using HTSeq-counts or cufflinks for example.
"Do I need to assemble the transcriptome first and then do blast search?" If no reference genome/annotation exists you will need to do this, first assemble your transcriptome (plenty of tools out there) then align against it and blast for your sequence of interest. Are you looking for genes by orthology, or are they known in the species?
If you give more specific information people will give clearer and more detailed ideas about how to proceed.
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