Extracting paired-end reads from assembly file

Question

[ankit hinsu]

Hi,

I have two paired-end read files. I made a combined de novo assembly of both in CLC and it gave me around 150,000 contigs. Out of all this, I want to extract reads constituting some 200 contigs.

What is the best approach for doing so?

Thank you in advance!

Answer 1

[Antonio R. Franco]

I assume you only need to map your reads with these 200 contigs After that, the extraction of the reads from the resulting BAM/SAM file has been described here in the forum many times

[ankit hinsu]

That is what I wanted....Thanks a lot..