Question: What tools can I use to calculate sequencing depth and sequencing coverage for ddRADseq data
0
gravatar for jingjin2203
22 months ago by
jingjin220330
jingjin220330 wrote:

Hi All, I have some ddRADseq data, I would like to know what are some tools that I can use to calculate the sequencing depth (the number of times that each base has been sequenced) and the sequencing coverage (the percentage of the whole genome that has been sequenced). Hope to get some advice here. Thanks in advance!

sequencing alignment next-gen • 1.5k views
ADD COMMENTlink modified 22 months ago by geek_y9.7k • written 22 months ago by jingjin220330
2
gravatar for geek_y
22 months ago by
geek_y9.7k
Barcelona/CRG/London/Imperial
geek_y9.7k wrote:

You can use genomeCoverageBed to get the coverage at each base in the genome and also later you can calculate the percentage of genome sequenced.

If you are using the stacks pipeline, you could also calculate the coverage per loci, number of loci sequenced etc.

ADD COMMENTlink written 22 months ago by geek_y9.7k
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: 1497 users visited in the last hour