0 out of 66386 passed blat criteria

[thestarocean]

I was running RNAeditor on my RNA-seq data. Although there is indeed content in both editingSites.alu.gvf and editingSites.nonalu.gvf, I notice the log with information:

STATUS: [Thu 03 Aug 2017 08:43:02 AM ] Search non uniquely mapped reads STATUS: [Thu 03 Aug 2017 08:43:02 AM ] Blat finished STATUS: [Thu 03 Aug 2017 08:43:02 AM ] Parse Blat output to look for non uniquely mapped reads STATUS: [Thu 03 Aug 2017 08:43:02 AM ] Analyse Blat hits (Slow) STATUS: [Thu 03 Aug 2017 08:43:02 AM ] Deleting invalid variants STATUS: 0 out of 66386 passed blat criteria STATUS: 66386 Missmatches had fewer than 2 missmatching-Reads. STATUS: 0 Missmatches had more missaligned reads than correct ones.

Is this a common problem? I use GATK version 3.5 with java 1.7 following your instruction.

[djhn75]

Yes i already recognised this message, but if the editingSites.nonalu.vcf file is not empty you can ignore this message. It seems that under specific conditions the counter for passed reads is not incremented. Where working on a solution for this problem. Thanks for your feedback, greetings David