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

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

Thank you in advance.


assembly • 217 views
ADD COMMENTlink modified 7 months ago by h.mon23k • written 7 months ago by Ric190
gravatar for h.mon
7 months ago by
h.mon23k 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 7 months ago by h.mon23k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2303 users visited in the last hour