Hello, I've got some questions with my RNA-seq results generated by galaxy.
For the experiment, I have a control group and a KO group (n=3), and I tried to look at the differential expressing genes between the two.
For data processes, i just simply mapped my reads back to the mm10 mouse genome, and then used the aligned files for Cuffdiff. For Cuffdiff, I analysed the data in two ways as described below:
1. First time, I ran cuffdiff on my RNA-seq data with one chromosome at a time (generated by UCSC) as the transcripts reference, and I generated 22 files.
2. Second time, I used the igenome_genes as the transcripts reference.
However, when i compared the result of the two, using method 1, it has picked up a lot more significant genes (~40 genes more) than method 2, and some of those genes found in method 1 is different to method 2, I just cant figure out what is the reason behind that gives such different results?
Sorry if my description isn't clear enough.
Thanks for the help,