I mapped my RNA-se reads with Tophat with the commands
Tophat –p 8 –o output –I 20000 –g 5 –G gtf_file Genome Fastq1 fastq2
Then I assembled the aligned tophat bam file using cufflinks with the commands
Cufflinks –p 20 –o output accepted.bam file
I found some of the genes are not assembled and they are masked as can be seen in skipped.grf.
I wonder why this has happened…?? Can anybody suggest something