Gtf/Gff File Of Repetitive Elements To Use With Tophat2
0
0
Entering edit mode
9.4 years ago
dfernan ▴ 710

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!

gtf tophat2 • 2.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 1249 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6