Hello,
Thanks for the effor to make the tools avaiable to bioinformatics community. I am currently replicating the analysis mention in your paper to learn this tool . However, I am having the following error message that I have no clue about how to interpret :
Start CIRCexplorer 1.0.6
Start to convert fustion reads...
Converted 138505 fusion reads!
Start to annotate fusion junctions...
Traceback (most recent call last):
File "CIRCexplorer-1.0.6/CIRCexplorer.py", line 459, in
annotate_fusion(ref_f, temp1, temp2)
File "CIRCexplorer-1.0.6/CIRCexplorer.py", line 64, in annotate_fusion
genes, gene_info = parse_ref1(ref_f) # gene annotations
File "CIRCexplorer-1.0.6/CIRCexplorer.py", line 203, in parse_ref1
genes[chrom] = Interval(genes[chrom])
File "/usr/local/lib/python2.7/dist-packages/interval.py", line 279, in init
raise TypeError("lower_bound is not hashable.")
TypeError: lower_bound is not hashable.
The corresponding command is :
1.tophat2 -a 6 --microexon-search -m 2 -p 10 -G /home/k/Downloads/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2013-03-06-11-23-03/Genes/genes.gtf
/home/k/Downloads/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
/home/k/Downloads/ncbi/public/sra/SRR901967.fastq
2.bamToFastq -i tophat_out/unmapped.bam -fq tophat_out/unmapped.fastq
3./home/k/Downloads/tophat-2.0.9.Linux_x86_64/tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search /home/k/Downloads/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome tophat_out/unmapped.fastq
4.CIRCexplorer.py -f tophat_fusion/accepted_hits.bam -g /home/k/Downloads/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -r /home/k/Downloads/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2013-03-06-11-23-03/Genes/refFlat.txt