I have RNA sequencing files and i want to check the gene expression of all genes from that file?
I want to know how can i get genes from that rna sequence files? Although it is a basic question but I am new to this type of work so asking.
DOES NM_001195025.1 this id represents a gene? or i have to extract a gene by giving some specific coordinates. How can I define that from this to that region is a gene? R genes only the exons?
Using the Tophat software suite is probably going to be the easiest and best way for you to go. Thankfully the authors of that software wrote a paper describing how it can be used with your data:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/
I know about tophat but i want to know :
What are genes in the transcriptome file?
I have to extract them by using some specific coordinates or by default the ids given are the gene ids?e.g: is this some gene id or i have to extract genes
NM_001195025.1
I totally agree that TopHat and Cufflinks will do the work. But, since you do not have previous experience on RNA-seq analysis, I recommend you to try first RobiNA (http://mapman.gabipd.org/web/guest/robin). With this software, using a very intuitive GUI, you will be able to give a first look to your file and genes of interest.
The ID you asked about: "NM_001195025.1" indeed represents a gene identifier. It is a refseq transcript ID.You can look these up in the NCBI database. There are online tools and tools in R that can help you transform these gene identifyers to the gene IDs you are more familiar with.
If these identifiers are in your file, than I guess you have a file with aligned RNA-sequencing data. You still need to normalize your data before you have gene expression information you can work with. Check the Limma and EdgeR Bioconductor packages, you can use these for normalization of your data and statistics. If you are familiar with R, you can use these.
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