Question: Coverage after an assembly ?
0
gravatar for Picasa
23 months ago by
Picasa350
Picasa350 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 • 457 views
ADD COMMENTlink modified 23 months ago by Sej Modha2.9k • written 23 months ago by Picasa350

Aren't all the output files explained right here?

ADD REPLYlink written 23 months ago by 5heikki7.3k
0
gravatar for Sej Modha
23 months ago by
Sej Modha2.9k
Glasgow, UK
Sej Modha2.9k 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 23 months ago by Sej Modha2.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 690 users visited in the last hour