How to run tophat without gff file for bacterial genome
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Entering edit mode
6.9 years ago
bassanio ▴ 40

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?

RNA-Seq tophat bacterial gene expresssion • 2.1k views
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Entering edit mode
6.9 years ago
Asaf 8.6k

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

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