cufflinks RNA-seq analysis

[liweixie]

I ran RNA-seq fq data by tophat to generated the accepted_hits.bam file. I want to use cufflinks to assemble transcript. But, I am not sure when I put cufflinks command, it just stop there.
Command: $cufflinks accepted_hits.bam
Please give me some help.

[min1204]

This protocol is very useful.

Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protocols 7, 562-578

[liweixie]

I had this paper on my hand. analysis starts to stop at cufflinks.

This protocol is very useful.

Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protocols 7, 562-578