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

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.

gtf rna-seq
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updated by Ram Ram • written by Munmun • Munmun

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).

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written by Benn Benn

1 answer

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.

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written by Mehmet Mehmet

True. Should move that to answer.

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written by ATpoint ATpoint

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