I had met several questions about the new pipeline, and I hope can get your help. (1) NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERYANNOTATIONANNOTATE (fust1_3:circexplorer2) and NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERYANNOTATIONANNOTATE (fust1_2:merged) , I can not see the difference from the two, about the command line, and the results are also similar. (2) NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERYANNOTATIONCOMBINE_GTFS. I think there maybe some errors? the command is like

sort -k 1,1 -k3,3n -k4,4n -u fust1_2.gtf fust1_1.gtf cel_N2_1.gtf cel_N2_2.gtf cel_N2_3.gtf fust1_3.gtf > annotation.combined.gtf

, but the third column is type of circRNA, not the start . I think there maybe

sort -k 1,1 -k4,4n -k5,5n

. NFCORE_CIRCRNACIRCRNAQUANTIFICATION:COMBINE_TRANSCRIPTOME_GTFS also have the same mistakes.

1. It will be identical if only one discovery tool is active. Differences will come into place once you use multiple discovery tools and perform a majority vote