How to extract DEGs from ".genes.fpkm_tracking" and ".isoforms.fpkm_tracking" files

Question

[Hamidreza Hashemi]

Hi All,

I hope you are all safe and healthy. Basically, I have no experience with RNAseq data analysis and I have received some data in the ".genes.fpkm_tracking" and ".isoforms.fpkm_tracking" format and have no idea how to extract them to create a heatmap for DEGs. I really appreciate it if someone could provide some instruction or tell me where to look to find such instruction.

Take Care, Hamid

[Ram]

Welcome to the crazy world of RNAseq. You should really try to get your hands on raw counts. FPKM is not comparable between samples and most robust DE analysis is performed on raw counts.

Heatmaps may come into play much later. DE analysis gives you statistically significant DE genes while heatmaps are a fancy way of showing nothing in particular.

[Carlo Yague]

Hi, while I agree with the two comments above (be careful with that data if you don't know how it was generated), have you tried, out of curiosity, to open the files with a simple text editor (notepad, textedit, etc...) ? More often than not, fancy file extension in bioinformatics are just text file.

Answer 1

[i.sudbery]

These files come out of CuffDiff. To extract the differentially expressed genes, CuffDiff should also have output a file called gene_exp.diff. If you need to call differential expression yourself, CuffDiff also outputs files call gene.count_tracking which can be used with DEseq or edgeR to call differential expression.