Processing single-end Bismark output file(s) (SAM format):
1_ATCACG_L001_R1_001_bismark_bt2.bam	2_CGATGT_L001_R1_001_bismark_bt2.bam	3_TTAGGC_L001_R1_001_bismark_bt2.bam	4_TGACCA_L001_R1_001_bismark_bt2.bam	5_ACAGTG_L001_R1_001_bismark_bt2.bam	6_GCCAAT_L001_R1_001_bismark_bt2.bam	7_CAGATC_L001_R1_001_bismark_bt2.bam	8_ACTTGA_L001_R1_001_bismark_bt2.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 >>1_ATCACG_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 1_ATCACG_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 1_ATCACG_L001_R1_001_bismark_bt2.bam:	618
Total number duplicated alignments removed:	5 (0.81%)
Duplicated alignments were found at:	5 different position(s)

Total count of deduplicated leftover sequences: 613 (99.19% of total)

Checking file >>2_CGATGT_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 2_CGATGT_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 2_CGATGT_L001_R1_001_bismark_bt2.bam:	594
Total number duplicated alignments removed:	4 (0.67%)
Duplicated alignments were found at:	4 different position(s)

Total count of deduplicated leftover sequences: 590 (99.33% of total)

Checking file >>3_TTAGGC_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 3_TTAGGC_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 3_TTAGGC_L001_R1_001_bismark_bt2.bam:	623
Total number duplicated alignments removed:	4 (0.64%)
Duplicated alignments were found at:	4 different position(s)

Total count of deduplicated leftover sequences: 619 (99.36% of total)

Checking file >>4_TGACCA_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 4_TGACCA_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 4_TGACCA_L001_R1_001_bismark_bt2.bam:	615
Total number duplicated alignments removed:	4 (0.65%)
Duplicated alignments were found at:	4 different position(s)

Total count of deduplicated leftover sequences: 611 (99.35% of total)

Checking file >>5_ACAGTG_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 5_ACAGTG_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 5_ACAGTG_L001_R1_001_bismark_bt2.bam:	623
Total number duplicated alignments removed:	4 (0.64%)
Duplicated alignments were found at:	4 different position(s)

Total count of deduplicated leftover sequences: 619 (99.36% of total)

Checking file >>6_GCCAAT_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 6_GCCAAT_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 6_GCCAAT_L001_R1_001_bismark_bt2.bam:	608
Total number duplicated alignments removed:	5 (0.82%)
Duplicated alignments were found at:	5 different position(s)

Total count of deduplicated leftover sequences: 603 (99.18% of total)

Checking file >>7_CAGATC_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 7_CAGATC_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 7_CAGATC_L001_R1_001_bismark_bt2.bam:	602
Total number duplicated alignments removed:	3 (0.50%)
Duplicated alignments were found at:	3 different position(s)

Total count of deduplicated leftover sequences: 599 (99.50% of total)

Checking file >>8_ACTTGA_L001_R1_001_bismark_bt2.bam<< for signs of file truncation...


Output file is: 8_ACTTGA_L001_R1_001_bismark_bt2.deduplicated.bam


Total number of alignments analysed in 8_ACTTGA_L001_R1_001_bismark_bt2.bam:	621
Total number duplicated alignments removed:	2 (0.32%)
Duplicated alignments were found at:	2 different position(s)

Total count of deduplicated leftover sequences: 619 (99.68% of total)