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LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq
http://starchimp.readthedocs.io/en/latest/
MIT License
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circRNA step2.sh bugs #20

Closed nongbaoting closed 6 years ago

nongbaoting commented 6 years ago 
-> % bash ./Step2.sh
Filtering out chimeric reads that appear circular
Filtering circular reads based on assigned thresholds of 5 reads in 10 individuals
awk: cmd. line:1: { if (5 >= var) print /storage/nong/pipeline/test/starchip/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

a bug, this should be a syntax error

kippakers commented 6 years ago

Hi, yes I just put in a fix to this bug last night. Updating to the latest version should fix it for you.

kippakers commented 6 years ago

Hi again Nongbaoting,

Apologies, I hadn't fully fixed that bug 3 hours ago, but it is fixed now. Sorry for the confusion!