How to extract this information

Question

[Lauren]

Hi there,

I am a beginner in bioinformatics and I would like the following information but do not know how to manipulate cufflinks gtf files (produced in galaxy) to in order to get it....

I would like gene_id, gene_name, chromosome number and start position of the gene and then FPKM counts of each of my samples all in one table.

What is the best way of reading in these gtf files, extracting this information?

thanks

Lauren

[seidel]

GTF files do not have FPKM values. If you walk through an example RNA Seq workflow in Galaxy, and google around a bit, you may be able to get some understanding. This question is a little too general (similar to "How do I do RNA Seq in Galaxy?"). I think you need to try a few things to build up a little knowledge so you can ask a more meaningful and specific question, and we can help you better.