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Old 07-17-2018, 06:04 AM   #1
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Location: India

Join Date: Jan 2016
Posts: 1
Default 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:
[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..
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gtf annotation file, rnaseq, tophat 2

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