Hi everyone, I have a question when using tophat-fusion-post, and any suggestions would be greatly appreciated.
I use the tophatfusion-0.1.0 (the old version) to do the tophat-fusion and the results seems fine. But when I use the tophat-fusion-post:
The error shows:
The one who occur the same error said it's the reason of Bowtie index and then I tried the Bowtie1 Bowtie2 index separately and even tried to use tophat2 to run my tophat-fusion-0.1.0 results but the errors are all the same. (link here: http://www.biostars.org/post/show/47...ion-post-error).
And my directory structure is:
I don't know where the question is, please give me some suggestions...
Thank you,
Conan.
I use the tophatfusion-0.1.0 (the old version) to do the tophat-fusion and the results seems fine. But when I use the tophat-fusion-post:
Code:
python /share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /share_bio/panfs/zengchq/baij/HumanRef/BowtieIndex_hs37.67
Code:
[Fri Jun 29 16:15:22 2012] Beginning TopHat-Fusion post-processing run (v0.1.0 (Beta)) ----------------------------------------------- [Fri Jun 29 16:15:22 2012] Extracting 23-mer around fusions and mapping them using Bowtie [Fri Jun 29 16:15:22 2012] Filtering fusions Processing: tophat_N/fusions.out Traceback (most recent call last): File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 1904, in <module> sys.exit(main()) File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 1875, in main filter_fusion(params) File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 632, in filter_fusion filter_fusion_impl(fusion_file, refGene_list, ensGene_list, ensGtp_dic, seq_chr_dic, fusion_gene_list) File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 351, in filter_fusion_impl kmer_len = len(seq_chr_dic.keys()[0]) IndexError: list index out of range
And my directory structure is:
Code:
(top_dir) Tophat-N Tophat-T tophatfusion_out - the output directory by tophat-fusion-post ensGene.txt ensGtp.txt refGene_sorted.txt mcl blast_human - blast database
Thank you,
Conan.
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