What tools can I use to calculate sequencing depth and sequencing coverage for ddRADseq data
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!
• 4,286 views
•
link
updated
by
GouthamAtla
•
written
by
jingjin2203 •
•
written
by
jingjin2203 •
1 answer
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.
• 0 views
•
link
written
by
GouthamAtla
Log in to answer this question.
More posts like this
-
How do I calculate read depth of sequencing?
written by Madde •
-
Fold80 Penalty value vs PCT > 0.2*mean
written by deniselavezzari •
-
Getting total sequenced megabases for each sample
written by zizigolu
-
what is the conventional apporach to calculate depth of coverage?
written by serpalma.v •
-
Freebayes usage of --haplotype-length and --max-complex-gap
written by jingjin2203 •
-
ddRADseq sequencing depth
written by jingjin2203 •
-
BED tool output
written by jaishridgl •
-
Calculate percentage of bases covered less than nX in targeted sequencing experiment
written by Ram
-
Quality of whole genome sequencing and whole exome sequencing
written by devinliao0918 •
-
Total Number Of Mapped Bases In Exome Ngs Data
written by User6891
