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.
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.