Getting transcripts from BAM file with gene names

Question

[Asaf]

I have RNA-seq data of E. coli and I'm trying to do a very simple thing (or so I thought), I'm trying to get a list of transcripts and for each transcript list the genes found in it (one gene or more in case of an operon).

I tried using cufflinks with -g, I get the names of the genes but the coordinates of the transcripts are the same as in the reference GTF file, not much help in identifying UTRs, operons etc.

I tried cufflinks without a reference and then merge the reference and the resulting gtf file with cuffmerge but the results weren't good at all.

Is there another tool that allows identifying transcripts and assigning gene names for them?

Thanks

Answer 1

[Asaf]

Apparently Rockhopper is the tool I was looking for, it manages bacterial RNA-seq from fastq to differential expression and gives the transcripts UTRs and operons as part of the output.

Thanks Brian ;)