Question: Getting An Error When Running Tophat-Fusion-Post
gravatar for Andrew
7.6 years ago by
Andrew10 wrote:

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:


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>

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!

bioinformatics tophat rna-seq • 3.8k views
ADD COMMENTlink modified 6.0 years ago by Paul1.4k • written 7.6 years ago by Andrew10
gravatar for mknut
7.6 years ago by
mknut90 wrote:

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.

ADD COMMENTlink written 7.6 years ago by mknut90
gravatar for Paul
6.0 years ago by
European Union
Paul1.4k wrote:

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,


ADD COMMENTlink written 6.0 years ago by Paul1.4k
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