Hi,
I am working on RNA sequencing and I run tophat. It seems that everything is ok but when I want compare junction bed generated from tophat with original ref.bed (convert gff to bed format), the result is completely different and almost no similarity exist. By the way two form bed file was generated by tophat. one with --no-novel-juncs option and another is total and when compare these two files about 1500 new junction found that seems ok. anyone knows what is the problem?thanks
I am working on RNA sequencing and I run tophat. It seems that everything is ok but when I want compare junction bed generated from tophat with original ref.bed (convert gff to bed format), the result is completely different and almost no similarity exist. By the way two form bed file was generated by tophat. one with --no-novel-juncs option and another is total and when compare these two files about 1500 new junction found that seems ok. anyone knows what is the problem?thanks