Processing paired-end Bismark output file(s) (SAM format):
zr2096_6_s1_R1_bismark_bt2_pe.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>zr2096_6_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

...passed!
Output file is: zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_6_s1_R1_bismark_bt2_pe.bam:	517
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 517 (100.00% of total)