I have been working on building a transcriptome for HAdV5. My process has been as follows:
1) use bowtie2-build to make HAdV reference genome index
2) map reads of HeLA infected cells (found online) using Tophat2 (gene annotated file was also found online, so I used --transcriptome-index option).
3) use Cufflinks on the generated accepted_reads.bam file
Now I'm pretty sure that steps 1 and 2 have been done correctly and that the formatting etc is all correct. The problem I have is that after running cufflinks, my transcripts.gtf file is 0 bytes and is blank. The other files produced are there but are extremely small and do not contain much in them (maybe a line or two). I don't get any errors when running Cufflinks so I'm wondering if anyone has some incite on what is going on? The command I used in cufflinks was: cufflinks -p 3 -o cuff_all accepted_reads.bam (note that accepted_reads.bam is in the same file as all the other files I have created and used in my attempt to make this transcriptome).
Let me know if you need any additional information, thanks!