Dear All,

I am looking for isoform diversiy and the ratio of intron and exon for each transcriptome in RNAseq data set. I did DEXSeq with intron and exonic parts together. I want to get the junctions.bed output from TopHat2 to run it in DEXSeq as well.

For that I need to convert the junctions.bed to gtf that has linked between junctions and the parent genes. Do you think if I use bedtools complement to get the gtf will be correct to use it in DEXSeq or do you have any idea how to convert this junctions.bed to be used in DEXSeq?

Many thanks in advance,

Rahel