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CIRIexplorer2 annotate

I am using CIRIexplorer2 to find the circRNAs. First I have done alignment and parsing. Now I am running the annotating command. But it gives error.

The command according to program is;

CIRCexplorer2 annotate -r gegeannotation.txt -g GENOME -b file.bed

Error: ValueError: need more than 2 values to unpack strong text

I have used .gtf annotation file which comes in place of REF but they have suggested to use .txt for gene annotation file. Could anybody tell me, how can I convert it from gtf to txt format? or If somebody have used the CIRIexplorer2 program?

circrnas ciriexplorer2
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updated by Barry Digby Barry Digby • written by HaroonPakistan • HaroonPakistan

2 answers

I have used .gtf annotation file which comes in place of REF but they have suggested to use .txt for gene annotation file. Could anybody tell me, how can I convert it from gtf to txt format? or If somebody have used the CIRIexplorer2 program?

For future users ..

gtfToGenePred -genePredExt -geneNameAsName2 <species>.gtf <species>.genepred
perl -alne '$"="\t";print "@F[11,0..9]"' <species>.genepred > <species>.txt

https://github.com/YangLab/CIRCexplorer2/issues/43

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written by Barry Digby Barry Digby

I solved, first do indexing through bowtie and then run the tophat2 command (can be seen on manual) for the alignment. Then do parsing and following analysis

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written by HaroonPakistan • HaroonPakistan

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