KeyError CIRCexplorer.py

[emanuele982]

Hi, thanks for sharing your useful tool. I'm currently attempting to repeat your example analysis, however I am having the following error message: Traceback (most recent call last): File "/usr/local/bin/CIRCexplorer.py", line 495, in fix_fusion(ref_f, genome_fa, temp2, output, options['--no-fix']) File "/usr/local/bin/CIRCexplorer.py", line 128, in fix_fusion fusions, fusion_names, fixed_flag = fix_bed(input_f, ref, fa, no_fix) File "/usr/local/bin/CIRCexplorer.py", line 324, in fix_bed iso_starts, iso_ends = ref['\t'.join([gene, iso, chrom, strand])] KeyError: 'Usp9x\tNM_009481\tchrX\t+'

Could you please help to fix the problem? I really appreciate any help you can provide.

I appreciate any help you can provide

[kepbod]

Could you offer your command line?

[emanuele982]

Hi thanks for your quick reply, here the command line I used:

tophat2 -a 6 --microexon-search -m 2 -p 8 -G gencode.vM4.annotation.gtf -o tophat2 bowtie2_index_mm10 _1.fastq,_2.fastq

tophat2 -o tophat_fusion -p 8 --fusion-search --keep-fasta-order --bowtie1 --fusion-read-mismatches 1 --no-coverage-search bowtie_index_mm10 tophat2/unmapped.fastq

CIRCexplorer.py -f accepted_hits.bam -g genome.fa -r <(sed -e '1d' refFlat_mm10.txt) --tmp -o CIRC_out

2015-05-18 4:25 GMT+02:00 Xiao-Ou Zhang notifications@github.com:

Could you offer your command line?

— Reply to this email directly or view it on GitHub https://github.com/YangLab/CIRCexplorer/issues/6#issuecomment-102896298.

[kepbod]

I suspect there are some problems in your refFlat_mm10.txt file, but I am not sure. Could you send your refFlat_mm10.txt to me (kepbod@gmail.com)?