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9.0 years ago
xf
•
0
Hi everyone,
These days I wanna to find gene fusions from my RNA-seq data,
mMy directory structure:
1-top_direcory
2-tophat_sample
2-refGene.txt
2-ensGene.txt
2-blast(soft symbolic link)
Command line:
tophat-fusion-post --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /index_bowtie/hg19
First, I encounter this error:
tophat-fusion-post --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 index_bowtie/hg19
[Mon Apr 6 23:50:35 2015] Beginning TopHat-Fusion post-processing run (v2.1.0)
-----------------------------------------------
[Mon Apr 6 23:50:35 2015] Extracting 23-mer around fusions and mapping them using Bowtie
samples updated
[Mon Apr 6 23:52:18 2015] Filtering fusions
Processing: tophat_weiai/fusions.out
Traceback (most recent call last):
File "/usr/local/tophat-2.0.10.Linux_x86_64/tophat-fusion-post", line 2644, in <module>
sys.exit(main())
File "/usr/local/tophat-2.0.10.Linux_x86_64/tophat-fusion-post", line 2615, in main
filter_fusion(bwt_idx_prefix, params)
File "/usr/local/tophat-2.0.10.Linux_x86_64/tophat-fusion-post", line 708, in filter_fusion
filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)
File "/usr/local/tophat-2.0.10.Linux_x86_64/tophat-fusion-post", line 556, in filter_fusion_impl
gene1, gene1_name, gene1_where, gene1_belong, gene1_sense, ens_gene1, ens_gene1_name = find_gene(chr1, coord1, dir[0], True)
File "/usr/local/tophat-2.0.10.Linux_x86_64/tophat-fusion-post", line 548, in find_gene
result.append(gene_exists(gene_list, chr, coord, one_dir, is_left))
File "/usr/local/tophat-2.0.10.Linux_x86_64/tophat-fusion-post", line 340, in gene_exists
if chr_order[chr] < chr_order[ref_chr]:
KeyError: '1'
Then, I check my fusion.out and ensGene.txt,refGene.txt. I found it maybe cause by "chr". So, I delete all the "chr" in the 2 txt [les ensGene.txt |awk 'gsub(/chr/,""){print }'
]
I rerun this, but I found the potential_fusion.txt
and result.txt
is empty.
[Tue Apr 7 00:05:54 2015] Beginning TopHat-Fusion post-processing run (v2.1.0)
-----------------------------------------------
[Tue Apr 7 00:05:54 2015] Extracting 23-mer around fusions and mapping them using Bowtie
samples updated
[Tue Apr 7 00:06:43 2015] Filtering fusions
Processing: tophat_weiai/fusions.out
0 fusions are output in ./tophatfusion_out/potential_fusion.txt
[Tue Apr 7 00:06:49 2015] Blasting 50-mers around fusions
[Tue Apr 7 00:06:49 2015] Generating read distributions around fusions
[Tue Apr 7 00:06:49 2015] Reporting final fusion candidates in html format
num of fusions: 0
-----------------------------------------------
[Tue Apr 7 00:06:49 2015] Run complete [00:00:55 elapsed]
I'm a little confused that it means this sample didn't have any fusion or something wrong with my steps?
Any advice will be appreciated,
Thanks