CIRIexplorer2 annotate

Question

[HaroonPakistan]

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?

Answer 1

[Barry Digby]

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

Answer 2

[HaroonPakistan]

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