Question: What tools can I use to calculate sequencing depth and sequencing coverage for ddRADseq data
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gravatar for jingjin2203
2.9 years ago by
jingjin220340
jingjin220340 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 • 2.2k views
ADD COMMENTlink modified 2.9 years ago by geek_y11k • written 2.9 years ago by jingjin220340
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gravatar for geek_y
2.9 years ago by
geek_y11k
Barcelona
geek_y11k 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 2.9 years ago by geek_y11k
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