after my successful following your protocol, using the same sample repeat, I have a lot of problems as following,
./Step1.sh
Filtering out chimeric reads that appear circular
Filtering circular reads based on assigned thresholds of 5 reads in 1 individuals
Argument "29219chr1" isn't numeric in subtraction (-) at /root/starchip/scripts/circles/merge_close_crna_1file.pl line 26, <> line 1211.
creating circRNA fasta and gtf for re-alignment and quantification
[fai_load] build FASTA index....
./Step2.sh
Creating a count matrix. This may take a long time for very large cohorts.
annotating your cRNA
Error: requested chromosome 0 does not exist in the genome file /root/files/circular/gencode.v28.primary_assembly.annotation.gtf.exons.genome. Exiting.
Use of uninitialized value $p2Info in split at /root/starchip/scripts/circles/summarize_geneinfo.pl line 12, <> line 1.
Use of uninitialized value in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 20, <> line 1.
Use of uninitialized value in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 20, <> line 1.
Use of uninitialized value $p1Distance in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 24, <> line 1.
Use of uninitialized value $p1Distance in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 24, <> line 1.
less circRNA.5reads.1ind.genes
ID Gene(s) Exon1 Exon2 Strand SpliceType
chr17:20204333-20205912 NA NA Exon-Exon
chr19:17276495-17276909 NA NA Exon-Exon
chr21:8209679-8254315 NA NA Exon-Exon
chr21:8209832-8254261 NA NA Exon-Exon
chr21:8209995-8254866 NA NA Exon-Exon
chr21:8395628-8441484 NA NA Exon-Exon
chr21:8441146-8441260 NA NA Exon-Exon
chr8:130152736-130180880 NA NA Exon-Exon
chrX:140783175-140784659 NA NA Exon-Exon
GL000220.1:109971-110121 NA NA Exon-Exon
after my successful following your protocol, using the same sample repeat, I have a lot of problems as following,
./Step1.sh Filtering out chimeric reads that appear circular Filtering circular reads based on assigned thresholds of 5 reads in 1 individuals Argument "29219chr1" isn't numeric in subtraction (-) at /root/starchip/scripts/circles/merge_close_crna_1file.pl line 26, <> line 1211. creating circRNA fasta and gtf for re-alignment and quantification [fai_load] build FASTA index.... ./Step2.sh Creating a count matrix. This may take a long time for very large cohorts. annotating your cRNA Error: requested chromosome 0 does not exist in the genome file /root/files/circular/gencode.v28.primary_assembly.annotation.gtf.exons.genome. Exiting. Use of uninitialized value $p2Info in split at /root/starchip/scripts/circles/summarize_geneinfo.pl line 12, <> line 1. Use of uninitialized value in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 20, <> line 1. Use of uninitialized value in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 20, <> line 1. Use of uninitialized value $p1Distance in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 24, <> line 1. Use of uninitialized value $p1Distance in string eq at /root/starchip/scripts/circles/summarize_geneinfo.pl line 24, <> line 1.
less circRNA.5reads.1ind.genes ID Gene(s) Exon1 Exon2 Strand SpliceType chr17:20204333-20205912 NA NA Exon-Exon chr19:17276495-17276909 NA NA Exon-Exon chr21:8209679-8254315 NA NA Exon-Exon chr21:8209832-8254261 NA NA Exon-Exon chr21:8209995-8254866 NA NA Exon-Exon chr21:8395628-8441484 NA NA Exon-Exon chr21:8441146-8441260 NA NA Exon-Exon chr8:130152736-130180880 NA NA Exon-Exon chrX:140783175-140784659 NA NA Exon-Exon GL000220.1:109971-110121 NA NA Exon-Exon
help me,thanks Chris Lou