I have a gene and I want to investigate its expression in different organs.
I'm not sure how best to do this though. I am thinking of using Bowtie2 to either:
- Align the transcript of the gene to the transcriptome for a cell in that organ (the RNA-seq data for a cell in an organ will be obtained from NCBI' SRA).
- Align the cell transcriptome to the genome of the organism.
Please could someone advise on what to do?
I then want to repeat the process using transcriptomes of cells from different organs and use DESeq2 to look at differential expression of the gene in each organ.