An error bothered me when I was doing STARChip circle detection on example data. I run Step1.sh fully according to the instruction but I got the error message:
Filtering out chimeric reads that appear circular
Filtering circular reads based on assigned thresholds of 5 reads in 1 individuals
awk: cmd. line:1: { if (5 >= var) print /home/xxyy/Public/Bio_data/RNA_seq/XXXX/circRNA/starchip-master/example/STARChip-circRNA/scripts/circles/circle_star.sh >> var2 }
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: { if (5 >= var) print /home/xxyy/Public/Bio_data/RNA_seq/XXXX/circRNA/starchip-master/example/STARChip-circRNA/scripts/circles/circle_star.sh >> var2 }
awk: cmd. line:1: ^ syntax error
cut: rawdata/cRNA.cutoff.5: No such file or directory
creating circRNA fasta and gtf for re-alignment and quantification
Previously, I followed the instructions to download the annotation file (.gtf) and genome file (.fa), run setup.sh and then starchip-circles.pl, which finally generated Step1.sh and Step2.sh. All these steps went smoothly.
Actually, I also run starchip-circles.pl starting from .fastq files with my own data and got the same error message.
An error bothered me when I was doing STARChip circle detection on example data. I run Step1.sh fully according to the instruction but I got the error message:
Previously, I followed the instructions to download the annotation file (.gtf) and genome file (.fa), run setup.sh and then starchip-circles.pl, which finally generated Step1.sh and Step2.sh. All these steps went smoothly.
Actually, I also run starchip-circles.pl starting from .fastq files with my own data and got the same error message.
I truly appreciate any help. Thanks in advance!