TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file

Question

[Munmun]

I'm running TopHat v2.1.1 on Mycobacterium tuberculosis genome using the gtf file download from the EnsemblBacteria FTP. When trying map to genome I get a warning:

[2018-07-17 11:55:54] Beginning TopHat run (v2.1.1)
[2018-07-17 11:55:54] Checking for Bowtie
          Bowtie version:    2.3.4.1
[2018-07-17 11:55:54] Checking for Bowtie index files (genome)..
[2018-07-17 11:55:54] Checking for reference FASTA file
[2018-07-17 11:55:54] Generating SAM header for /exthome/users/rna_seq/bowtie2/ref
[2018-07-17 11:55:54] Reading known junctions from GTF file
    Warning: TopHat did not find any junctions in GTF file
[2018-07-17 11:55:54] Preparing reads

I want to know what might be the reason for this warning. And what should be done to avoid this. Any idea please let me know.

[Benn]

The reason for the warning is probably because your bacterium does not have exon junction in its genome. To avoid this you can use another aligner or eukaryotic genome (which has exon junctions).

[Sej Modha]

I'd suggest that you should use HISAT2 or STAR instead of TopHat2.

HISAT2 or Tophat2

Answer 1

[Mehmet]

Tophat and Hisat2 are splicer aligner, therefore there must be intron-exon junction. In bacteria, as you know, there is no intron.

I suggest you use not splicer aligner; such as Bowtie2.

[ATpoint]

True. Should move that to answer.