I am new to Molecular biology and Bioinformatics. I am starting a project where I need to get Transcriptome data and RNA-seq data. Could you guys please help me understand the difference between RNA-seq and Transcriptome? I was able to get Transcriptome data from NCBI SRA database, but where can I find RNA-seq data? Another question I have is about infering expression of genes based on RNA-seq- How do we get the expression profile of any genes based on RNA-seq? or can we use transcriptome data instead? Please help me understand.
I would suggest you read wikipedia pages about transcriptome and RNA-seq. Get some basic background about these terms and then you will automatically answer your questions. Read below.
Could you guys please help me understand the difference between RNA-seq and Transcriptome?
Transcriptome data refers to data that is used to measure expression level of transcripts. There are different methods that can be used to generate transcriptome data For e.g., microarray , RNA-seq, RT-PCR, EST tags etc.
I was able to get Transcriptome data from NCBI SRA database, but where can I find RNA-seq data?
RNA-seq data can be downloaded from SRA too. Which transcriptome data did you download?
Another question I have is about inferring expression of genes based on RNA-seq- How do we get the expression profile of any genes based on RNA-seq? or can we use transcriptome data instead? Please help me understand.
If you are using RNA-seq then you will have to perform alignment against the reference genome and then quantify the expression level of genes based on some gene model. Search Biostars, there are plenty of posts about it.
