remapping input should be Unmapped.out.mate or mate of PE?

dieterich-lab / circtools

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

http://circ.tools

GNU General Public License v3.0

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remapping input should be Unmapped.out.mate or mate of PE? #92

Open genebial opened 2 years ago

genebial commented 2 years ago

Excuse me for a sec. In the slurm_circtools_detect_paired_mapping.sh, it is recommended to remap the Unmapped.out.mate from the 1st mapping, respectively. But in the "Manual mapping process" part, it is recommended to remap the Sample1_1.fastq.gz, which is one of the pair ends reads. I am confused. Which one should take? THANK YOU for your time.