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Old 12-19-2013, 04:05 AM   #1
sivarajank
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Location: India

Join Date: Nov 2013
Posts: 1
Question Tophat Fusion Post Doesn't Report Fusions

Hi All,

I'm working on mouse transcriptome data, single end reads from Ion torrent system.

I wanted to identify fusion candidates with the help of tophat-fusion and executed the below commands.

1. tophat2 -p 10 -o ./tophat_out_against_chr_bowtie1_with_fusion --fusion-search --bowtie1 ../mouse_chr_seqs/index/mm_chr_index abc.fastq
2. tophat-fusion-post -p 10 -o ./tophat_fusion_out_chr --non-human --num-fusion-reads 1 --num-fusion-pairs 0 --num-fusion-both 5 ../mouse_chr_seqs/index/mm_chr_index

After running tophat2, I got few fusions, however after running tophat-fusion-post, I don't get anything the potential_fusions file or the result file.

Could some one help me in getting the issue resolved....???

Thanks a lot.!

P.S.:
1. I followed the directory structure identically as explained in tophat website and in the forums.
2. I tried changing num-fusion-pairs to zero, as my reads are NOT paired end.
3. Path to all the tools like bowtie, samtools, tophat, etc. are set properly
4. Folder naming conventions are properly followed (Beginning with tophat)

The O/P of Tophat-fusion-out:
Beginning TopHat-Fusion post-processing run (v2.1.0)
-----------------------------------------------
[Thu Dec 19 17:30:02 2013] Extracting 23-mer around fusions and mapping them using Bowtie
[Thu Dec 19 17:30:03 2013] Filtering fusions
Processing: tophat_out_with_fusion_search_against_chromosome/fusions.out
0 fusions are output in ./tophat_fusion_out_chr/potential_fusion.txt
[Thu Dec 19 17:30:04 2013] Blasting 50-mers around fusions
[Thu Dec 19 17:30:04 2013] Generating read distributions around fusions
[Thu Dec 19 17:30:04 2013] Reporting final fusion candidates in html format
num of fusions: 0
-----------------------------------------------
[Thu Dec 19 17:30:04 2013] Run complete [00:00:01 elapsed]

Cheers,
Sivarajan.
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Sivarajan, K
Project Fellow,
Centre For Cellular And Molecular Biology,
Hyderabad, India.
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Old 09-22-2014, 12:46 PM   #2
Auction
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Location: california

Join Date: Jul 2009
Posts: 24
Default

Same problem also happened in my dataset, does anyone know the answer?

Thanks.
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