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
Error: segment-based junction search failed with err =-6
segment_infix.h:81 Assertion failed : data_begin_position <= data_end_position was: 18446744073709551615 >
What am I missing here?