Hi, was just wondering whether TopHat-HTSeq-DESeq is an appropriate workflow for finding changes in retroelements / other repetitive elements in a mouse KO vs WT cell line?
Are repetitive sequences filtered out at the alignment (TopHat), counting (HTSeq), or comparison (DESeq) stages?
I am using the ensembl gtf file - do gtf files contain most of the known non-coding / retrolement sequences in them?
Thanks
Alex
Are repetitive sequences filtered out at the alignment (TopHat), counting (HTSeq), or comparison (DESeq) stages?
I am using the ensembl gtf file - do gtf files contain most of the known non-coding / retrolement sequences in them?
Thanks
Alex