DV200 Fragment Quality
Calculate the share of RNA fragments longer than a user-selected cutoff.
Description
DV200-style summaries count fragments longer than a size cutoff.
DV200-style summaries count fragments longer than a size cutoff. This tool weights by supplied fragment frequencies and allows a cutoff other than 200 nt.1
Calculate the share of RNA fragments longer than a user-selected cutoff.
When to use DV200 Fragment Quality
Use this tool to calculate the share of RNA fragments longer than a user-selected cutoff.
Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
How to use DV200 Fragment Quality and understand its results
- Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
- Enter fragmentSizesNt, fragmentCounts, minimumLengthNt using the field table and calculation rules, then run the tool.
- Read qualifyingFragments, totalFragments, dv200Percent. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| fragmentSizesNt | Fragment sizes nt | list of number | Required |
| fragmentCounts | Fragment counts | list of number | Required |
| minimumLengthNt | Minimum length nt | number | Required |
Enter aligned nonempty nonnegative sizes/counts with positive total frequency and a finite cutoff. Include only sizes strictly greater than the cutoff. Return qualifying/total fragments and percentage under the dv200Percent key; use 200 for that conventional cutoff.
qualifying=Σcount_i for size_i>cutoff; percent=100 qualifying/totalCounts Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| qualifyingFragments | Qualifying fragments | number |
| totalFragments | Total fragments | number |
| dv200Percent | Dv 200 percent | number |
{
"input": {
"fragmentSizesNt": [
100,
250,
300
],
"fragmentCounts": [
10,
20,
30
],
"minimumLengthNt": 200
},
"output": {
"qualifyingFragments": 50,
"totalFragments": 60,
"dv200Percent": 83.33333333333334
}
}Limitations and assumptions
This does not integrate an electropherogram or weight by RNA mass. Equal-to-cutoff fragments are excluded, and a different cutoff changes the meaning of the named output.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Insert Size Mode: Find the modal insert size, breaking ties toward the shorter fragment. For a complementary task, use Gene Body Coverage Bias: Detect 3-prime RNA coverage bias from aggregated end-of-gene read depth.
References
-
DV200 Fragment Quality — tool.io
Similar or alternative tools
- Insert Size Mode
Find the modal insert size, breaking ties toward the shorter fragment.
- Gene Body Coverage Bias
Detect 3-prime RNA coverage bias from aggregated end-of-gene read depth.