comparison repmatch_gff3.xml @ 13:d31ef9abce74 draft default tip

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12:34d134cd4ca9

 * **Step Size** - Distance for each iteration.
 * **Replicates** - Minimum number of replicates that can be matched for a match to occur.  This value must be at least 2.
 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.

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13:d31ef9abce74

 * **Step Size** - Distance for each iteration.
 * **Replicates** - Minimum number of replicates that can be matched for a match to occur.  This value must be at least 2.
 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.

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**Output Data Files**

 * **Data MP** - gff file consisting of only peak pairs

  - Columns are **chr**, **script**, **blank**, **peak start**, **peak end**, **blank**, **normalized tag counts**, **blank** and **info**.
  - Peak start and end are separated by one coordinate.
  - Normalized tag is the occupancy averaged across replicates.
  - Attributes include C-W distance, sum total of tag counts, number of replicates merged.

 * **Data D** - tabular file consisting of the list of all matched replicates.
 * **Data UP** - tabular file consisting of all unmatched peak-pairs.

**Output Statistics Files**

 * **Statistics Table** - tabular file providing the description key of **Data D**.
 * **Statistics Histogram** - graph of the number of matched locations having the indicated replicate counts.

**Comments on Replicates**

Three types of replicates may be considered.  Biological replicates represent independently collected biological samples.
At least two biological replicate must be performed for each experiment from which a conclusion is being drawn, and the
conclusion must be evident in both biological replicates when analyzed separately.  Technical replicates represent a re-run
of the assay on the same biological material.  This is usually done when one replicate fails to produce quality data, and is
used to replace that earlier replicate.  Sequencing replicates represent additional sequencing of the same successful library
in order to obtain more reads should the analysis require it.  The reads from individual sequencing replicates are usually
merged without need for separate analysis.

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