Entering edit mode
7.7 years ago
BioGeek
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170
Sorry to bother you all. I am newbie to NGS. Does the PacBio Reads only contain positive (+) strand or both (+/-) strand?
All DNA synthesis based sequencing technologies produce reads that are in
5' --> 3'orientation. One infers the other strand based on this data.Bit confused and caffeine deprived, but, the positive and negative strand is a convention based on coordinates on the chromosome, but the fact that polymerase works in 5' --> 3' direction is not strand-specific (for WGS). WGS will contain reads from both strands, regardless of the orientation of sequencing technology, no?
While post above is correct on its own the point about "+" strand was not addressed.
A single strand of DNA is called
"Sense (+)"if an RNA version of the strand is translated or translatable into protein (WikiPedia link).But that definition doesn't match with the notation in e.g. a GTF file, in which an entire gene can be on either - or + strand. In that notation, '+' would mean that your start codon has a lower coordinate than your stop codon, with '-' vice versa.
Are you talking about IsoSeq transcriptome sequencing or genome sequencing?
PacBio long reads genome sequencing.
Did you get a concrete answer for your question?. I am wondering the same thing, I believe all the Isoforms are in the positive strand ...