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Hey Everybody.
I am new at Illumina sequencing and RRBS.
Just to check if I'm going right.
When I run a 36 cycles at Illumina it means I will get 36 bp reads, since only one base is read per cycle. Even I'm not reading all the fragment (for example 100 bp) I understand that we have a random sheared DNA that can be aligned and the overlaps will complete the sequence.
2 things I do not understand:
- The sequences of the adapters are sequencend, aren't they? It won't use to much of the 36 bp?
- For RRBS we do not have this random sheared of DNA. The DNA is cut in specific sites, which means I do not have the other fragment to cover the rest of the fragment after 36 bp
ATCGTAC site of enzymeCGGCTGATCGATCG... 50 bp
ATCGTAC site of enzymeCGGCTGATCGATCG... 50 bp
If there is no other site for the enzyme until 50 bp, 14 bp will be no covered
Am I crazy?
I am new at Illumina sequencing and RRBS.
Just to check if I'm going right.
When I run a 36 cycles at Illumina it means I will get 36 bp reads, since only one base is read per cycle. Even I'm not reading all the fragment (for example 100 bp) I understand that we have a random sheared DNA that can be aligned and the overlaps will complete the sequence.
2 things I do not understand:
- The sequences of the adapters are sequencend, aren't they? It won't use to much of the 36 bp?
- For RRBS we do not have this random sheared of DNA. The DNA is cut in specific sites, which means I do not have the other fragment to cover the rest of the fragment after 36 bp
ATCGTAC site of enzymeCGGCTGATCGATCG... 50 bp
ATCGTAC site of enzymeCGGCTGATCGATCG... 50 bp
If there is no other site for the enzyme until 50 bp, 14 bp will be no covered
Am I crazy?