Question: normalizing count data metagenome
0
gravatar for PLSA
3.1 years ago by
PLSA0
PLSA0 wrote:

Hi,

I have two metagenomes and did assembly reads to contigs, and also mapped reads back to contigs. I need to know the difference in abundance of sequences could be assigned to particular genomes and the functional capacities of species in two metagenomes.

The point is the contigs can have different number of reads re-mapped.

My question is how can I normalize the sequencing depth of two data to see the difference between them? For example, data1: 5 contigs -> species A data2: 3 contigs -> species B => species A could be more than species B in data1

but

data1: 5 contigs (number of reads re-covered are 5,10,30,5,50) -> species A data2: 3 contigs (number of reads re-covered are 60,30,40) -> species B => it could be species B are more abundant than species A in data 2

Any one can help or suggest? Thanks in advance.

PLSA

sequencing genome • 1.1k views
ADD COMMENTlink written 3.1 years ago by PLSA0
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: 1703 users visited in the last hour