9
votes
Accepted
How to validate that BAMs have been downloaded correctly?
samtools quickcheck is all you need. From the manual:
Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header ...
- 19.8k
4
votes
Accepted
Where can I visualize Ramachandran plot?
Here is a page with several suggested methods. I agree that Rampage looks the best of the options, but it seems that it provides some suggested workflows for drawing it in R so that it is very ...
- 4,212
3
votes
Difference between clinical significance and statistical significance
This is non-parametric statistics, the mean requires conformation to the normal distribution (but there are exceptions), or perhaps better put it requires a fixed relationship between mean and ...
M__♦
- 12.8k
3
votes
Accepted
Verify a predicted protein in one genome in a different genome of the same species
This should be very easy to do. Here are some options:
Use a tool like Exonerate or GeneWise that can align protein sequences to genomic DNA while attempting to model splice sites etc.
As you said, ...
- 10.5k
2
votes
Generating simulated gold standard NGS dataset/ Any publicly available smal gold standard NGS dataset
I would suggest subsampling an existing dataset such as the GIAB resource that you've already indicated.
Use a utility such as seqtk to subsample the appropriate number of reads from the dataset, and ...
- 4,212
2
votes
Is there a standard method to validate whether a bigWig file is correct?
There's no standard validation method, but a simple one would be python -c "import pyBigWig; bw = pyBigWig.open('your_file.bw'); print(bw.IsBigWig());". If you get <...
- 19.8k
2
votes
Accepted
Difference between clinical significance and statistical significance
Another viewpoint could be : statistically significant implies use of sampling theory to establish presence of significant difference between case and control groups. The "clinical " significance ...
- 202
1
vote
Metagenomic shotgun data with internal control
The problem with correlations in relative scale is know on the literature, it has been suggested to change to other metrics. So I wouldn't use it for internal control.
As you can see on figure 3 of ...
- 4,723
1
vote
Accepted
Is there a standard method to validate whether a bigWig file is correct?
As noted in another answer, it's relatively easy to tell if a file is bigWig or not by opening it up with, say, standard UCSC Kent utilities like bigWigToBedGraph ...
- 3,184
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