Question: SparseAssembler inward or outwards reads
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gravatar for Ric
4 months ago by
Ric190
Australia
Ric190 wrote:

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

Thank you in advance.

Michal

assembly • 170 views
ADD COMMENTlink modified 4 months ago by h.mon21k • written 4 months ago by Ric190
0
gravatar for h.mon
4 months ago by
h.mon21k
Brazil
h.mon21k wrote:

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.

ADD COMMENTlink written 4 months ago by h.mon21k
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