Hi All.
I have a question about Tophat. I mapped the RNA-Seq by both Tophat and Bowtie. When running Tophat, a GTF file of gene annotations was provided. I found some reads were mapped by Bowtie but not Tophat. These reads seem to fall into the regions lack of gene annotation. Does Tophat remove such reads because they fall outside the annotated regions when providing GTF file?
Any reply will be appreciated.
Best
I have a question about Tophat. I mapped the RNA-Seq by both Tophat and Bowtie. When running Tophat, a GTF file of gene annotations was provided. I found some reads were mapped by Bowtie but not Tophat. These reads seem to fall into the regions lack of gene annotation. Does Tophat remove such reads because they fall outside the annotated regions when providing GTF file?
Any reply will be appreciated.
Best