which strand PacBio sequence?

Question

[midox]

Hello,

I wanted to know the sequences of PacBio are given from one strand of DNA or not? for the treatment I need to do every time the reverse-complement? Thank you

[GenoMax]

All sequencing technologies that I know of sequence DNA in 5'-->3' orientation. No matter what strand.

[midox]

are you sure all reads have the same orientation? if it's exact. So it's not important to do the reverse complement.

[GenoMax]

See this for clarification.

[midox]

ok thanks for the link but it is not very clear. "The ccs program takes multiple reads of the same SMRTbell sequence and combines them to produce one high quality consensus sequence." ok it takes many reads in the two direction like the figure but the direction of the consensus it is not clear and the consensus of what strand come from Up or down strand??

thanks

[midox]

so the representation of reads in FASTA file in one orientation? or in 5'-->3' and 3'-->5' the two???

Answer 1

[Antonio R. Franco]

PacBio uses a proprietary adapter that contains a bubble so both strands from a same DNA fragment can be sequenced

[midox]

so the representation of reads are from the same strand of DNA? or I have to duplicate each reads in reverse-complement?

[Antonio R. Franco]

See genomax2 latest comment ..