Question: After Novo assembly
1
gravatar for lamlam
3.4 years ago by
lamlam10
lamlam10 wrote:

After assembling (novo assembler ) a sequence of Tuberculosis I found that the number of base pair is greater than that number of base pair is the reference strain Is this logical?

assembly • 830 views
ADD COMMENTlink modified 3.4 years ago by genomax71k • written 3.4 years ago by lamlam10

Is this logical?

Yes.

And computational biology is a quantitative science. Please tell us exactly how much greater your assembly is and which reference genome you have used.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by piet1.7k

i used Mycobacterium tuberculosis H37Rv this reference has 4.4Mb and my sequence has 7.3 Mb?

ADD REPLYlink written 3.4 years ago by lamlam10
1

Have you tried to compare the two to see how the assemblies are different? Use Mauve to compare.
Did you have an excess of sequence (> 100x gross coverage) that went into this assembly?

ADD REPLYlink written 3.4 years ago by genomax71k
1

Yes, you should map your contigs to the refseq and then identify contigs which do NOT map. Blast these contigs to identify their origin. Furthermore, your may plot GC-content of your contigs versus coverage. Do you see more than one cluster in the scatter plot?

ADD REPLYlink written 3.4 years ago by piet1.7k
0
gravatar for RamRS
3.4 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

There could be any number of reasons resulting in an increase in the number of bases - duplication at various levels, insertions, etc. Why is comparing base count any kind of metric?

ADD COMMENTlink written 3.4 years ago by RamRS24k
1

Why is comparing base count any kind of metric?

Tuberculosis genomes are extremely well conserved, much more than any other bacterial species.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by piet1.7k
1

Ah, I see. Thank you :)

ADD REPLYlink written 3.4 years ago by RamRS24k
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: 1495 users visited in the last hour