Question: Coverage after an assembly ?
0
gravatar for Picasa
2.4 years ago by
Picasa390
Picasa390 wrote:

Hi,

My output from the assembler SOAPdenovo2 is formatted like this

scaffold148 17.4

scaffold149 37.1

What is that second number ? Is it the coverage ? If yes I don't understand what it means in an assembly.

I mean the coverage is normally the number of time that a base is represented/sequenced. What does it mean in that case ??

assembly • 521 views
ADD COMMENTlink modified 2.4 years ago by Sej Modha3.9k • written 2.4 years ago by Picasa390

Aren't all the output files explained right here?

ADD REPLYlink written 2.4 years ago by 5heikki7.9k
0
gravatar for Sej Modha
2.4 years ago by
Sej Modha3.9k
Glasgow, UK
Sej Modha3.9k wrote:

To find out whether the second column represents coverage info, you can align the reads back to the soap2 contigs, calculate the coverage for each contig using mpileup and compare the coverage info.

ADD COMMENTlink written 2.4 years ago by Sej Modha3.9k
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