yanglab / circexplorer Goto Github PK

according to the instruction, I do multiple mapping with tophat using the format
tophat2 -a 6 --microexon-search -m 2 -p 10 -G knownGene.gtf -o tophat hg19_bowtie2_index RNA_seq.fastq
the program went wrong, and show error information:
error retrieving prep-reads info

what does that mean? how can I solve it? please help!

Hi there,

When I use pip install CIRCexplorer, I can install sucessfully. But when I call CIRCexplorer.py, i got the following message:

Traceback (most recent call last):
  File "/home5/jhuang/software/anaconda3/bin/CIRCexplorer.py", line 7, in <module>
    from circ.CIRCexplorer import main
  File "/home5/jhuang/software/anaconda3/lib/python3.6/site-packages/circ/CIRCexplorer.py", line 31, in <module>
    from genomic_interval import Interval
ModuleNotFoundError: No module named 'genomic_interval'
jhuang@pauper:~/projects/Misc/drought-stress/CIRCexplorer$ CIRCexplorer.py
Traceback (most recent call last):
  File "/home5/jhuang/software/anaconda3/bin/CIRCexplorer.py", line 7, in <module>
    from circ.CIRCexplorer import main
  File "/home5/jhuang/software/anaconda3/lib/python3.6/site-packages/circ/CIRCexplorer.py", line 31, in <module>
    from genomic_interval import Interval
ModuleNotFoundError: No module named 'genomic_interval'

When I try to install through conda, I got the following warning that did not success:

Fetching package metadata .............
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - circexplorer -> python 3.4* -> xz 5.0.5
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

I also tried install from source, but no luck.

Any idea how I can fix?

Thanks in advance!

See http://stackoverflow.com/questions/25337706/setuptools-vs-distutils-why-is-distutils-still-a-thing

unique mapping with TopHat-Fusion, tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index tophat/unmapped.fastq, can i use bowtie2 to mapping with TopHat-Fusion?

Hi,
I found CIRCexplore a very useful tool for detecting circRNA from RNA-seq. I am interested in detecting circRNA which completely falls in intron (=lariat sequence). I mapped the paired-end reads with tophat and executed this program in the same way as mentioned on github page, but I did not find circRNA associated with lariats, rather from exons. Can you suggest me if some how the tool can enforced to pic circ RNA only from introns.

Thanks.

I have run the tophat commands and generated bams using tohat2 fusion search on the unmapped fastq.
However, running them with the CIRCexplorer now gives the error - "Please make sure sample is BAM!"

Does the bam file obtained from tophat2 fusion need to be processed in any other way before passing it to the CIRCexplorer

Thanks

Hi,
When I run the CIRCexplorer at last step using standard parameters, sth wrong happened, how could it happen?
thanks!

Start to convert fustion reads...
Converted 30234 fusion reads!
Start to annotate fusion junctions...
Traceback (most recent call last):
File "/home/program/bin/CIRCexplorer.py", line 371, in
annotate_fusion(ref_f, temp1, temp2)
File "/home/program/bin/CIRCexplorer.py", line 53, in annotate_fusion
gene, isoform = parse_ref1(ref_f)
File "/home/program/bin/CIRCexplorer.py", line 166, in parse_ref1
ends = list(map(int, line.split()[10].split(',')[:-1]))
IndexError: list index out of range

I've solved it! This issue happened probabilistically and it was the error coming from server, not from the script.
Hope this answer could help anyone else.

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

Start CIRCexplorer 1.1.10
Start to convert fustion reads...
Converted 0 fusion reads!
Start to annotate fusion junctions...
Traceback (most recent call last):
File "/usr/local/bin/CIRCexplorer.py", line 9, in
load_entry_point('CIRCexplorer==1.1.10', 'console_scripts', 'CIRCexplorer.py')()
File "build/bdist.linux-x86_64/egg/circ/CIRCexplorer.py", line 508, in main

File "build/bdist.linux-x86_64/egg/circ/CIRCexplorer.py", line 68, in annotate_fusion

File "build/bdist.linux-x86_64/egg/circ/CIRCexplorer.py", line 209, in parse_ref1

ValueError: need more than 2 values to unpack

could someone pls tell me why i am getting 0 fusion reads converted and value error

Hi,
Thanks for providing such a great tool!
Just wondering did CIRCexplorer support paired end data? TopHat can align paired-end reads, but when I convert unmapped reads to PE fastq after sorted and indexed the bam file, there were very few reads converted successfully. But if I merged two paired end fastq (R and L) to give a single fastq file, CIRCexplorer worked good.
One more thing, can CIRCexplorer do secondary analysis of Chimeric.out.sam (output fusion detection data from RNA-STAR)? I tried to convert Chimeric.out.sam to Chimeric.out.bam, and input the bam file to CIRCexplorer, but I got nothing. I compared the output files from TopHat-Fusion and rna-star, they are very similar to each other, and it is kind of strange that CIRCexplorer got nothing from Chimeric.out.bam.
Thanks again for the effor to make the tools avaiable to bioinformatics community.

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

I am trying to use CIRCexplorer with STAR mapper and the error "IndexError: list index out of range" keeps occurring. I can't figure out how to remedy this problem, any help would be appreciated. Here is my command line:
python CIRCexplorer.py -j 0002-surg-funsion-junction.txt --genome=human.hg19.genome --ref=UCSC_Refseq_sno_miRNA_lncipedia_3_0_hg19_11-10-2014.gtf

Start CIRCexplorer 1.1.1
Start to annotate fusion junctions...
Traceback (most recent call last):
File "CIRCexplorer.py", line 494, in
annotate_fusion(ref_f, temp1, temp2)
File "CIRCexplorer.py", line 67, in annotate_fusion
genes, gene_info = parse_ref1(ref_f) # gene annotations
File "CIRCexplorer.py", line 201, in parse_ref1
start = starts[0]
IndexError: list index out of range

Hello,

I was wondering how circexplorer pick an isoform and then deduces which exons are included inside the circRNA? Knowing it only get information about the BSJ

Thank you!

Hello,
Im doing some tests with data set.
Followed the command lines suggested with tophat.
Fetched ref.txt with fetch_ucsc.py
And got:

Start CIRCexplorer 1.1.1
Start to convert fustion reads...
Converted 102717 fusion reads!
Start to annotate fusion junctions...
Traceback (most recent call last):
File "CIRCexplorer.py", line 494, in
annotate_fusion(ref_f, temp1, temp2)
File "CIRCexplorer.py", line 67, in annotate_fusion
genes, gene_info = parse_ref1(ref_f) # gene annotations
File "CIRCexplorer.py", line 206, in parse_ref1
genes[chrom] = Interval(genes[chrom])
File "build/bdist.linux-x86_64/egg/interval.py", line 279, in init
TypeError: lower_bound is not hashable.

Is there anything Im doing wrong?

Thanks in advance!