Hi all

From ENCODE database, I downloaded a sample of eCLIP experient on K562 against PUM2 (SRR5112018.sra). Then, I followed the steps in the protocol from the supplementary materials of Van Nostrand, Eric L , et al. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nature Methods (2016).

However, when I called peaks, I encountered some problems. I have tried more than twice but it is still the same.

When I run "clipper -b Boule2.demux.trim.round2.rmRep.rmDup.sorted.r2.bam -s mm9 -o Boule2.demux.trim.round2.rmRep.rmDup.sorted.r2.peaks.bed --bonferroni --superlocal --threshold-method binomial --save-pickle", I got the following message.

ERROR:root:peak finding failed:, ENSMUSG00000040985.7, boolean index did not match indexed array along dimension 0; dimension is 217 but corresponding boolean dimension is 80

Thank you in advance for your help.

Best regards