Getting An Error When Running Tophat-Fusion-Post
2
1
Entering edit mode
8.6 years ago
Andrew ▴ 10

I ran tophat with the following command:

tophat-2.0.3.Linux_x86_64/tophat2 -o ./tophat_pig -p 8 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search -r 50 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM /WPS/RNA/liangpeiquan/data/bowtie-0.12.8/indexes/Sus_scrofa  Sus_scrofa_1.fq Sus_scrofa_2.fq

And i got the usual result files.

Then, I want to run tophat-fusion-post,so i set my folders like this:

refgene.txt
ensgene.txt
mcl
tophat_pig
blast

and my tophat-fusion-post script.

/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5  /WPS/RNA/liangpeiquan/data/bowtie-0.12.8/indexes/Sus_scrofa

then i ran the shell script,but i got the commond like this:

[Wed Nov 21 10:27:09 2012] Beginning TopHat-Fusion post-processing run (v2.0.6)
[Wed Nov 21 10:27:10 2012] Extracting 23-mer around fusions and mapping them using Bowtie
[Wed Nov 21 10:31:45 2012] Filtering fusions
    Processing: tophat_pig/fusions.out

Traceback (most recent call last):
File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 2091, in <module>
sys.exit(main())

File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 2062, in main
filter_fusion(bwt_idx_prefix, params)

File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 700, in filter_fusion
filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)

File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 426, in filter_fusion_impl
kmer_len = len(seq_chr_dic.keys()[0])

IndexError: list index out of range

Can anybody give me a hand to solve this problem?

Thankyou very much!

rna-seq bioinformatics tophat • 4.1k views
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2
Entering edit mode
8.5 years ago
mknut ▴ 90

This question has been answered here: Tophat-Fusion-Post Error To sum up - put both bowtie 1 and bowtie 2 indexes in your index folder (/WPS/RNA/liangpeiquan/data/bowtie-0.12.8/indexes/ in your case). It worked for me and it seems to be working for others.

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Entering edit mode
7.0 years ago
Paul ★ 1.4k

Hello all,

please can you tell me where i will get mcl file??? I am not able to find it..

 

thank you for any help,

Paul.

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