The orientation of Pacbio read.

Question

[934963534]

I am quite new to bioinformatics. I know that paired-end short reads have original orientation and their reverse-complement reads. So are Pacbio reads only in the original orientation as the reference genome?

Any answer is appreciated!

Answer 1

[h.mon]

Paired-end DNAseq Illumina sequencing has forward-reverse orientation in relation to each other, but either read 1 or read 2 can have any orientation in relation to the reference genome. Single-end PacBio long reads, likewise, can have any orientation in relation to the reference genome.

Stranded RNAseq libraries add strand information to the sequencing - depending on the protocol, it can be the same strand as the mRNA, or the reverse mRNA strand. Notice that the strand information is related to the mRNA, not to the reference genome.

[934963534]

Thanks，it perfectly solved my problem.

[934963534]

Also, do you know how to build the de-Bruijn graph with the short reads of different orientation, I know a node can refer to the orignal kmer and its forward-reverse kmer, but how to deal with the problem that these short reads can also be in different orientation to the reference. For example, given genome reference AAACCT, should ACCT(TGGA) and TCCA(AGGT) considered also a same node in the de-Bruijn graph?

[h.mon]

This is an entirely new question, open a new post for it.