Gtf/Gff File Of Repetitive Elements To Use With Tophat2

Question

[dfernan]

Hi,

I am trying to estimate the expression of known repetitive elements.

I'd like to know what'd be an appropriate GTF file to give tophat as input for mapping reads to repetitive elements.

I have them as a bed file but I was wondering what'd be the right conversion to GTF for tophat:

chr1  3004832 3011092 - L1Md_F2
chr1  3027807 3033128 + L1Md_A
chr1  3054939 3060895 - L1Md_F2
chr1  3096316 3102490 - L1Md_F2
chr1  3227966 3233898 - L1Md_A
chr1  3334727 3341048 + L1Md_T

Note that the gene/transcript/exon model does not really follows here so I am not sure if that'd be a problem. Please let me know if you have some suggestions.

Thanks!