SparseAssembler inward or outwards reads

Question

[Ric]

Hello, How can I determine whether my reads are inward or outward paired-end reads?

Thank you in advance.

Michal

Answer 1

[h.mon]

If they are your reads, you can get this information by knowing the library prep kit and sequencing platform. The sequencing facility which did the work should provide you with this information.

However, if this information is lost forever, assemble a draft genome using the paired reads as single reads (MEGAHIT and Tadpole are two fast and good assemblers), then map the reads into this draft genome with BWA. Just by looking at BWA logs on the screen you will know the orientation of your reads.