visualization of contigs in PaDeNa

Dec 21, 2011 at 4:51 PM

Where can i find the number of contigs in padena? i was trying to found this information in the padena paper and technical guide, but i cant find it.

 

thanks for your responses,

 

LeonardoBio

Coordinator
Dec 21, 2011 at 8:10 PM

Hi LeonardoBio

I'm not entirely sure if I understand your question - I assume you are using PadenaUtil to assemble a set of sequences in a FASTA file. If so, you will know that when you run the application you can specify a file (which is very similar in fact to a FASTA file). For example:

PadenaUtil -k:32 -l -c:2 -o:outputfile.txt

In this case, if you look at outputfile.txt, you will see a set of contigs. There is no switch for PadenaUtil to tell you how many there are, you just have to count them (or write a simple script to do so).

 

Simon

Jan 24, 2012 at 11:14 PM

yes simon, this is my question, thanks for the reply, and forgive mi late response, i going to create a script to do that.