I' try to detect the differentially expressed gene using human RNASEQ data. And I don't care about the alternative splice and so on right now.
Could I just use tophat to map my reads and cuffdiff to deal with the bam file and get the DEG?
Or I must follow the tophat-cufflink-coffmerge-cuffdiff pipeline strictly?
I have got the gtf file from UCSC and iGenome.
Could I just use tophat to map my reads and cuffdiff to deal with the bam file and get the DEG?
Yes. You can. Since you already have gtf file, you don't need to do the reference-based transcriptome assembly.
Good luck.
To work with Cufflinks you may need to understand each step on this workflow:
http://cole-trapnell-lab.github.io/cufflinks/manual/
DEG are generated on the last step Cuffdiff and the plot are visualized in R using cummRbund. The advantage using Cufflinks is normalization is done directly by Cuffdiff.
Here are the command line to use the workflow. If you are not familiarized with them, you may consider use Galaxy.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics