Question: TopHat-fusion-post ERROR or Empty?
0
gravatar for xf
5.5 years ago by
xf0
China
xf0 wrote:

Hi everyone,

These days I wanna to find gene fusions from my RNA-seq data,

my directory structure like this:

+++++++++++++++++++++++++++++++++

1-top_direcory

  2-tophat_sample

  2-refGene.txt

  2-ensGene.txt

  2-blast(soft symbolic link)

++++++++++++++++++++++++++++++++++++++

Command line is :

+++++++++++++++++++

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 usi                        ng 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, fus                        ion_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_ge                        ne1_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 appreciate,

Thanks 

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