It seems that all the input files for mergeBAM.py are R2.

[yangqihang1230]

/home/data2/yqh/conda/envs/hic-pro/bin/python /home/data1/yqh/HIC/hicpro/HiC-Pro//HiC-Pro_3.1.0/scripts/mergeSAM.py -q 10 -t -v -f bowtie_results/bwt2/sample1/377Formation_R2.clean_A03.bwt2merged.bam -r bowtie_results/bwt2/sample1/377Formation_R2.clean_A03.bwt2merged.bam -o bowtie_results/bwt2/sample1/377Formation_R2.clean_A03.bwt2pairs.bam

mergeBAM.py

forward= bowtie_results/bwt2/sample1/377Formation_R2.clean_A03.bwt2merged.bam

reverse= bowtie_results/bwt2/sample1/377Formation_R2.clean_A03.bwt2merged.bam

output= bowtie_results/bwt2/sample1/377Formation_R2.clean_A03.bwt2pairs.bam

min mapq= 10

report_single= False

report_multi= False

verbose= True

Merging forward and reverse tags ...

1000000

2000000

3000000

4000000

5000000

Hello, this is the mergeBAM.py command I generated. Why are both the filenames for the -f and -r options set to R2? It should be one R1 and one R2, right?