Hello,
To measure expression of repetitive elements in my samples I mapped my reads to a .fa file containing one copy of each type of repetitive element, then ran the HT-Seq-edgeR pipeline on them - generating the U-shaped BCV plot below - can anyone explain this to me?
Out of curiosity I mapped my reads to the ref mouse genome then ran the HT-Seq-edgeR pipeline using a homemade gtf file listing the co-ordinates of promoters (i.e. counting read mapping to promoters) - which has generated the truly bizzare (to me) BCV plot below - I have no idea what it means and won't be inferring anything from it, but was wondering if anyone had seen anything like this before?
Thanks for any advice on either plot!
Alex
To measure expression of repetitive elements in my samples I mapped my reads to a .fa file containing one copy of each type of repetitive element, then ran the HT-Seq-edgeR pipeline on them - generating the U-shaped BCV plot below - can anyone explain this to me?
Out of curiosity I mapped my reads to the ref mouse genome then ran the HT-Seq-edgeR pipeline using a homemade gtf file listing the co-ordinates of promoters (i.e. counting read mapping to promoters) - which has generated the truly bizzare (to me) BCV plot below - I have no idea what it means and won't be inferring anything from it, but was wondering if anyone had seen anything like this before?
Thanks for any advice on either plot!
Alex