Bismark low mapping efficiency
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19 months ago
mailard • 0

Hi! I mapped methylome of HepG2 to reference human genome with bismark. Is report of bismark okey? Or i have some troubles in mapping? And I have the question about coverage of WGBS. Is it okey that mean coverage of only one chromosome is 10X? I use this code for coverage: samtools coverage -h int.bam

Thanks for your answer!

Sequence pairs analysed in total: 695666796 Number of paired-end alignments with a unique best hit: 133717953 Mapping efficiency: 19.2% Sequence pairs with no alignments under any condition: 548099782 Sequence pairs did not map uniquely: 13849061 Sequence pairs which were discarded because genomic sequence could not be extracted: 219

Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 66665199 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 67052535 ((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total: 0

Final Cytosine Methylation Report

Total number of C's analysed: 5669261795

Total methylated C's in CpG context: 153773530 Total methylated C's in CHG context: 5634249 Total methylated C's in CHH context: 54245515 Total methylated C's in Unknown context: 62135

Total unmethylated C's in CpG context: 205329168 Total unmethylated C's in CHG context: 1449704634 Total unmethylated C's in CHH context: 3800574699 Total unmethylated C's in Unknown context: 2788852

C methylated in CpG context: 42.8% C methylated in CHG context: 0.4% C methylated in CHH context: 1.4% C methylated in unknown context (CN or CHN): 2.2%

Bismark WGBS mapping methylome • 697 views

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