Dear all,
I like to check if someone here has experience on this mouse RNA-Seq data analysis.
This is the mouse RNA-Seq with 50SR. Users wanted to just see the gene expression difference between different type of treatments compared with control. They used mouse strain Balb/C. We used mm9 from UCSC as reference genome to perform the Bioinformatics analysis including the TopHat and DEseq. This week, users revealed that this strain information (with emphasizing not the regular C57BL6 strain) and pointed out this whole genome sequencing information available for this strain: http://www.sanger.ac.uk/resources/mouse/genomes/ and ftp://ftp-mouse.sanger.ac.uk/current_denovo. They want us to download Balb/C strain genome and used it as the reference genome for this RNA-Seq project. From above, I didn't see any gene annotation file associated with this particular strain. I wonder how much difference it could be using the different strain as reference genome. Anyway, this RNA-Seq only looks for the gene expression difference. I want to check with people here to see if we have to re-perform the data analysis with the new reference genome. If yes, where could we get the new gene annotation file for the mouse strain Balb/C?
Many thanks!
sincerely
ChristmasSunflower
I like to check if someone here has experience on this mouse RNA-Seq data analysis.
This is the mouse RNA-Seq with 50SR. Users wanted to just see the gene expression difference between different type of treatments compared with control. They used mouse strain Balb/C. We used mm9 from UCSC as reference genome to perform the Bioinformatics analysis including the TopHat and DEseq. This week, users revealed that this strain information (with emphasizing not the regular C57BL6 strain) and pointed out this whole genome sequencing information available for this strain: http://www.sanger.ac.uk/resources/mouse/genomes/ and ftp://ftp-mouse.sanger.ac.uk/current_denovo. They want us to download Balb/C strain genome and used it as the reference genome for this RNA-Seq project. From above, I didn't see any gene annotation file associated with this particular strain. I wonder how much difference it could be using the different strain as reference genome. Anyway, this RNA-Seq only looks for the gene expression difference. I want to check with people here to see if we have to re-perform the data analysis with the new reference genome. If yes, where could we get the new gene annotation file for the mouse strain Balb/C?
Many thanks!
sincerely
ChristmasSunflower
Comment