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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 ...
Devon Ryan's user avatar
  • 19.6k
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 ...
Maximilian Press's user avatar
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__'s user avatar
  • 12.5k
3 votes
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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, ...
terdon's user avatar
  • 10.2k
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 ...
Maximilian Press's user avatar
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 <...
Devon Ryan's user avatar
  • 19.6k
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 ...
Subhash C. Davar's user avatar
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 ...
llrs's user avatar
  • 4,713
1 vote
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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 ...
Alex Reynolds's user avatar

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