This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Help understanding bismark report BS-Seq

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!

bs-seq bismark

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.

0 answers

No answers yet.

Log in to answer this question.