How to run tophat without gff file for bacterial genome

Question

[bassanio]

I would like to find the RNA seq differential expression against bacterial genomes with out gff /gtf files. I used the following commands:

tophat -p 8 \
  -i 1 \
  -m 2 \
  --max-insertion-length 0 \
  --max-deletion-length 0 \
  -o STA3_WG \
  Geneome1_WG.fa \
  R1.fastq R2.fastq

And It throws error:

[2014-12-17 14:47:54] Searching for junctions via segment mapping
    [FAILED]
Error: segment-based junction search failed with err =-6
./SeqAn-1.3/seqan/sequence/

segment_infix.h:81 Assertion failed : data_begin_position <= data_end_position was: 18446744073709551615 >

What am I missing here?

Answer 1

[Asaf]

Since bacterial mRNAs don't have introns (at least the vast majority of them), you don't need to use tophat, use bowtie instead.