Hi, can you help me understand what the results from a bismark report mean?
I did the exercises i found in babraham bioinformatics and I got 3 reports, containing many plots and:
Alignment
Sequences analysed in total 199,733
Single-end alignments with a unique best hit 134,425
Sequences without alignments under any condition 11,640
Sequences that did not map uniquely 53,668
Genomic sequence context not extractable (edges of chromosomes)
Cytosine Methylation
Total C's analysed 1,494,509
Methylated C's in CpG context 110,062
Methylated C's in CHG context 6,840
Methylated C's in CHH context 12,109
Unmethylated C's in CpG context 344,434
Unmethylated C's in CHG context 374,058
Unmethylated C's in CHH context 647,006
Percentage methylation (CpG context) 24.2%
Percentage methylation (CHG context) 1.8%
Percentage methylation (CHH context) 1.8%
Alignment to Individual Bisulfite Strands OT 66,768 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 67,657 original bottom strand
Cytosine Methylation after Extraction
Total C's analysed 1,494,509
Methylated C's in CpG context 110,062
Methylated C's in CHG context 6,840
Methylated C's in CHH context 12,109
Unmethylated C's in CpG context 344,434
Unmethylated C's in CHG context 374,058
Unmethylated C's in CHH context 647,006
Percentage methylation (CpG context) 24.2%
Percentage methylation (CHG context) 1.8%
Percentage methylation (CHH context) 1.8%
M-Bias Plot (its a plot)
thank you very much!
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Exactly which part do you need help understanding? It's rather unreasonable to ask someone to write a long comprehensive reply if you only find one small thing confusing. Also, start by describing what YOU think it means, that's rather more efficient for those of us replying.
Apart from Devon's suggestion, please read the manual, esp. if you are a newcomer to bisulfite sequencing. Many of the doubts can be cleared easily by reading the manual carefully. https://rawgit.com/FelixKrueger/Bismark/master/Docs/Bismark_User_Guide.html