Problem with extracting circRNA sequences

[MSajek]

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, 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

[MSajek]

I found the reason. In the original genomic file chromosome names looks like:

chr1 1 chr10 10 chr11 11 chr12 12 chr13 13 chr14 14 chr15 15 chr16 16 chr17 17 chr18 18 chr19 19 chr2 2 chr20 20 chr21 21 chr22 22 chr3 3 chr4 4 chr5 5 chr6 6 chr7 7 chr8 8 chr9 9 chrM MT chrX X chrY Y When I change them to: chr1 chr10 .... everythink starts working