problems getting started with tophat-fusion-post

[tankman]

Hello,

Question from newbie at fusion detection. I'm trying to do 2 things:

1) replicate the example given on the tophat-fusion-post page to find fusion candidates;

2) try to figure out if I can really use tophat-fusion/post to find fusion candidates in only single-end data

As far as 1) is concerned, I've so far failed. I've replicated the directory structure and run tophat for the initial alignment with the given parameters, and then upon running tophat-fusion-post it finds 0 fusions. I think it's just not returning anything from the initial filtration, since it doesn't even attempt to blast anything. I'll quote the output at the end, any help would be really appreciated. Casual filtration of fusions.out reveals that there are events to report -- I have a feeling it's the mixing of single and paired end reads that's involved.

If anyone has an exact copy of all the commands they issued to both tophat and tophat-fusion-post that made the example work it would be probably most quickly clear things up for me.

Does anyone have any experience with 2), using tophat-fusion-post? any tips?

OUTPUT

[b01@node8-9 test_fusion]$ find . -name "fusions.out" -print
./tophat_MCF7/fusions.out
./tophat_BT474_mix_1.fastq/fusions.out
./tophat_BT474_mix_2.fastq/fusions.out
./tophat_SKBR3_mix_1.fastq/fusions.out
./tophat_SKBR3_mix_2.fastq/fusions.out
[b01@node8-9 test_fusion]$ which tophat-fusion-post
/packages/tophat/2.0.4/bin/tophat-fusion-post
[b01@node8-9 test_fusion]$ tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 index/hg19
[Thu Sep 27 13:55:07 2012] Beginning TopHat-Fusion post-processing run (v2.0.4)
-----------------------------------------------
[Thu Sep 27 13:55:07 2012] Extracting 23-mer around fusions and mapping them using Bowtie
samples updated
[Thu Sep 27 13:59:40 2012] Filtering fusions
Processing: tophat_BT474_mix_1.fastq/fusions.out
Processing: tophat_BT474_mix_2.fastq/fusions.out
Processing: tophat_MCF7/fusions.out
Processing: tophat_SKBR3_mix_1.fastq/fusions.out
Processing: tophat_SKBR3_mix_2.fastq/fusions.out
0 fusions are output in ./tophatfusion_out/potential_fusion.txt
[Thu Sep 27 14:00:54 2012] Blasting 50-mers around fusions
[Thu Sep 27 14:00:55 2012] Generating read distributions around fusions
[Thu Sep 27 14:00:55 2012] Reporting final fusion candidates in html format
num of fusions: 0
-----------------------------------------------
[Thu Sep 27 14:00:55 2012] Run complete [00:05:48 elapsed]


thanks!

[jp.]

Hi
Do you know how to use single-end tophat fusion ?
thank you

Hello,

Question from newbie at fusion detection. I'm trying to do 2 things:

1) replicate the example given on the tophat-fusion-post page to find fusion candidates;

2) try to figure out if I can really use tophat-fusion/post to find fusion candidates in only single-end data
...
num of fusions: 0
-----------------------------------------------
[Thu Sep 27 14:00:55 2012] Run complete [00:05:48 elapsed]


thanks!