Hello to everyone,
i am trying to analyze my RNAseq Data. So i follow the tutorial:
Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, 2020 Reference-based RNA-Seq data analysis (Galaxy Training Materials) . /training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
Just briefly: so i have my paired-end FASTQ files
I use STAR aligner with built-in MM10 Full genome, without gene model (nothing selected)
To calculate counts i used fetureCounts with buit-in MM10 or use .gtf file with Release M25 (GRCm38.p6)… Already here i have a bit different count numbers (built-in vs M25).
To identify DEGs i tried several tools. With DESeq2 i have more than 400 DEGs (FDR<0.05)
If i use EdgeR or limma-trend, then i have only few DEGs with FDR or adjusted p-values <0.05
So my question is why the number of DEGs are so extreamly different in different tools?
And another question if i need to specify gtf file during maping with STAR?
Thank you for your answers and help.