Cufflinks analysis of Tophat BAM file

Question

[qudrat]

Very often I see at the end of Cufflinks run Waiting for 1 threads to complete. [ ******* ] 99% and it takes too much time. Can somebody shed light on this

[Kevin Blighe]

You should check to see if the process is still running through the top command in linux (may be the same for MAC, too).

It is normal for it to get 'stuck' at 99% as it tidies up files and pieces everything back together. Transcriptome assembly is no easy feat.