Do the paired-end forward-reverse and reverse-forward (--fr and --rf) parameters work exactly the same in bowtie2? If not what's the difference between them?
-
-
No they are not the same. The first f(r) refers to the upstream mate and the second refers to the downstream mate.
Considering DNA structure (http://academic.brooklyn.cuny.edu/bi...ructure.html):
5'-------------3'
3'-------------5'
It depends on the sequencing technology. Whether it reads each strand of read from 5' end or 3' end.
For example, if it reads both strands from 5' end, the forward sequence will appear first so it is upstream mate and the reverse complement one is downstream. So we have:
Both from 5' => --fr
Both from 3' => --rf
One from 3' end and the other from 5' (both from one strand) => --ffLast edited by milad621; 10-14-2012, 09:41 AM.
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment