Which Kinds Of Pair-End Reads Direction Do We Have Now?

Question

[Chen Sun]

About the pair-end / mate-pair read, because of different technology they use, the normal read direction may be different.

As far as I know, there are directions --> <-- and <-- --> for different tech.

Is there any other possible direction of today's sequencing technology?

Answer 1

[Ashutosh Pandey]

SOLiD mate pair reads are oriented in the same direction: R3 ------> F3 ------>

Bowtie provides several options for paired end reads. Below is taken from bowtie2 manual:

--fr/--rf/--ff
The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. E.g., if --fr is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (-I and -X) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. --rf likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. --ff requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented. Default: --fr (appropriate for Illumina's Paired-end Sequencing Assay).