minzhe / clirc Goto Github PK

I try to use Clirc and I have a problem in the first step. When I try to extract circRNA sequences from my file with coordinates and reference genome that were used to detect circRNA i have the following error:

perl bin/Clirc_library.pl -coord /media/marcin/data/KasiasDataRean/RBP/edger/Clirc/DGEcircs.csv -genome /media/marcin/data/MartaAndAgaAnalysis/Genome/GRCh37_primary_assembly.fa -library /media/marcin/data/KasiasDataRean/RBP/edger/Clirc/lib.txt

• Start building alignment library. *
  Done extracting circRNA coordinates.
  Done indexing genome.
  The following region dose not exist: chr15 + 84228005 84228054 chr15_84228005_84257523:/media/marcin/data/KasiasDataRean/RBP/edger/Clirc/DGEcircs.csv
  Can't use an undefined value as an ARRAY reference at /home/marcin/programs/Clirc/bin//query.pl line 49, <FILE_IN1> line 1.
  Extracting circRNA sequences failed!

I used CIRI2 do detect circRNAs, circMeta package for annotation and DGE analysis and GRCh37_primary_assembly human genome from gencode.
I will be grateful for any help.
Best,
Marcin