I'm trying to get fusion post running on human data, yet fusion-post returns 0 fusions. These samples had been run using a different index, with a non-zero amount of fusion results, therefore I'm not sure why this isn't working. The g1k index however needs to be used on these samples, and I'm using the same index for fusion-post as was used for aligning the tophat reads. The directory setup apart from the index should otherwise be identical to the working setup.
My directory structure:
The blast directory contains symlinks to human_genomic, other_genomic and nt blast files. The index contains bowtie1 built human g1k index files (tophat with fusion was run using bowtie1).
I'm using the following parameters to run fusion-post on a cluster with 64GB of allocated memory to the job:
I get this output with 0 potential fusions (the fusions.out files in the sample directories are non-empty):
I feel like I've tried everything suggested in the other threads where people have had the same problem. Any ideas?
My directory structure:
Code:
tophat_299aM tophat_299bN tophat_299bT mcl ensGene.txt refGene.txt blast
Code:
[Tue Jan 15 11:49:19 2013] Beginning TopHat-Fusion post-processing run (v2.0.6) ----------------------------------------------- [Tue Jan 15 11:49:19 2013] Extracting 23-mer around fusions and mapping them using Bowtie [Tue Jan 15 11:54:09 2013] Filtering fusions Processing: tophat_299aM/fusions.out Processing: tophat_299bN/fusions.out Processing: tophat_299bT/fusions.out 0 fusions are output in ./tophatfusion_out/potential_fusion.txt [Tue Jan 15 11:55:06 2013] Blasting 50-mers around fusions [Tue Jan 15 11:55:06 2013] Generating read distributions around fusions [Tue Jan 15 11:55:06 2013] Reporting final fusion candidates in html format num of fusions: 0 ----------------------------------------------- [Tue Jan 15 11:55:06 2013] Run complete [00:05:47 elapsed]
Code:
tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 1 --num-fusion-both 0 bowtie1_g1k_idx/human_g1k_v37
Code:
drwxr-xr-x 7 user dir 131072 Jan 15 11:55 . drwxr-x--- 10 user dir 131072 Jan 16 10:30 .. drwxr-xr-x 2 user dir 131072 Jan 15 11:55 blast_genomic drwxr-xr-x 2 user dir 131072 Jan 15 11:55 blast_nt drwxr-xr-x 2 user dir 131072 Jan 15 11:55 check -rw-r--r-- 1 user dir 984352595 Jan 15 11:53 fusion_seq.bwtout -rw-r--r-- 1 user dir 154987245 Jan 15 11:49 fusion_seq.fa -rw-r--r-- 1 user dir 195266454 Jan 15 11:54 fusion_seq.map drwxr-xr-x 2 user dir 131072 Jan 15 11:55 logs -rw-r--r-- 1 user dir 0 Jan 15 11:55 potential_fusion.txt -rw-r--r-- 1 user dir 1120412 Jan 15 11:55 result.html -rw-r--r-- 1 user dir 0 Jan 15 11:55 result.txt -rw-r--r-- 1 user dir 18 Jan 15 10:19 sample_list.txt drwxr-xr-x 2 user dir 131072 Jan 15 11:54 tmp
Comment