Entering edit mode
6.9 years ago
felipead6
▴
10
I work with mouse genome and I have RNA-Seq data from a mouse strain. When I align the reads in the mouse genome, a gene is not quantified since this gene does not appear in the reference mouse genome. How can I quantify this gene?
You don't have to realign. Just add the gene of interest informations in the gtf file and rerun featurecounts (to count reads per gene) and then use edgeR or DESeq2.
That sounds interesting. How do I add the gene information in the .gtf file considering that I have the position of the gene available?
look at : http://www.ensembl.org/info/website/upload/gff.html for gtf column description, and add corresponding informations to the gtf (so open it in a text editor and edit it).
just open the gtf with gedit or excel and fill
Do not use excel please : https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-80
If the sequence is present and the annotation doesn't exist then this is indeed the correct approach!
I have the .gb file from genbank, is there any way to transform this to .gtf?
That part is easily googled:
e.g:
https://github.com/riverlee/genbank2gtf