Unknown Reads with Clark-S

[Mike]

Hi, 

I have built the spaced database for Clark-S and it did a great job classifying my sample!!!!

However, after running the estimate_abundance script on the results obtained from running the classify_metagenome script, I get a result file that shows that there are some unknown reads. It's about 7% of the reads. 

My question is: how can I pull those "unknown" reads, so I can run them through a de novo assembly ? 

In other words: is there a way to get the unknown reads from my sample? 

Thank you so much, 

Mike 

[Rachid OUNIT]

Hello Mike,

This can be an interesting option to add in "estimate_abundance" script. How would like these reads to be pulled out? 

Can you please detail what would be the input and output for to postprocess what you are looking for?

Thank you,

Cheers,

Rachid

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