What is the sequencing coverage recommended for somatic and germline mutations in whole genome and whole exome sequencing?
germline at least 30x, somatic depends on your question.
have a look at this paper: http://jmd.amjpathol.org/article/S1525-1578%2817%2930025-9/fulltext
I suggest a couple of readings for theory and some figures.
https://rtsf.natsci.msu.edu/_rtsf/assets/File/depth%20and%20coverage.pdf
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-195
We are successful with 100X paired end sequencing in whole exome analysis (Illumina 2500 plateform, sure selectec libraries).
Depends on the pipeline and analysis tools that are being used.
We have used 20X and got success, some people have no success with 70X.
The more coverage and depth you have, greater is the chance of success.
Best Wishes.
below 20x it should not be considered, especially cause now it´s quite easy to pull the average coverage around 100x.
we do 100X for control sample(blood for germline variation) and 300X for tumor sample.
200 x for somatic mutations in cancer samples and 50 x for germline mutations
How to distinguish Donor-specific Cell-free DNA from recipient Cell-free DNA when we have VCF file after performing next-generation sequencing.
01 February 2019 7,445 6 View
I am looking for tools to get basic statistics of contigs files from Illumina sequencing.
01 February 2017 2,811 5 View
Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...
03 March 2021 8,796 3 View
I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance
03 March 2021 3,568 1 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...
03 March 2021 1,401 3 View
I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...
03 March 2021 8,920 3 View
dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...
03 March 2021 6,994 5 View
1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...
03 March 2021 2,870 3 View
I'm dealing with a mediation model and am using the PROCESS module in SPSS. Due to SPSS and PROCESS being limited in the imputation methods - being unable to handle multiple imputation - the other...
02 March 2021 4,362 1 View
I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.
02 March 2021 4,359 3 View
If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis
02 March 2021 7,670 3 View