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lindaszabo / KNIFE

Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms
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KNIFE errors out with bam2fastq converted fastq files #13

Closed ShobanaSekar closed 6 years ago

ShobanaSekar commented 6 years ago

Hi,

I have been trying to run KNIFE v1.4 on some of our RNAseq data. For this dataset we did some UMI based dup marking on the bams and re-converted the dup marked bam to fastq in order to run KNIFE (and other circRNA tools) on them. When I try to run KNIFE on this bam2fastq converted inputs, I am running into this error:

Error in eval(predvars, data, env) : object 'is.pos' not found Calls: glm ... eval -> -> model.frame.default -> eval -> eval

(complete log file attached - KNIFE_out.log )

However I am able to run it successfully on the (non-dup mark converted) original fastq file itself. After I did the bam2fastq conversion I also made sure to trim them as pairs so only mates are retained but I am not sure why KNIFE is erroring out.

Is KNIFE incompatible with fastqs that have been generated this way?

Appreciate your help!

-Shobana

ShobanaSekar commented 6 years ago

I figured it out, I had the read_id_style as complete when it was in fact appended. Sorry about that. Closing the issue.