comparison cwpair2.xml @ 12:79a10fe09b66 draft default tip

Uploaded

11:6383cae47688

the specified percentage of this 95th percentile.  So if the peak at the 95th percentile has 200 tags, and "relative
threshold" 50 is used, then it will not consider any peak having less than 100 tags.

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**Output Data Files**

 * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E).  The tag count sum is reported in column F, along with the C-W distance in bp in column I.
 * **closest/largest/mode O** - tabular file containing the Orphans (all peaks that are not in pairs).
 * **closest/largest/mode D** - tabular file containing the Details, which lists + and – strand information separately.  The start and end represent the lower and higher coordinates of the exclusion zone from GeneTrack, and “Value” is the tag count sum within the exclusion zone.  The peak pair midpoint is calculated along with the distance between the two paired peaks (midpoint-to-midpoint or C-W distance).

 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
 * **closest/largest/mode F** - pdf file that provides the final plots graph.
 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).

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**Options**

 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
 * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
 * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.

    </help>
    <expand macro="citations" />
</tool>

12:79a10fe09b66

the specified percentage of this 95th percentile.  So if the peak at the 95th percentile has 200 tags, and "relative
threshold" 50 is used, then it will not consider any peak having less than 100 tags.

-----

**Options**

 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
 * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
 * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
 
-----

**Output Data Files**

 * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E).  The tag count sum is reported in column F, along with the C-W distance in bp in column I.
 * **closest/largest/mode O** - tabular file containing the Orphans (all peaks that are not in pairs).
 * **closest/largest/mode D** - tabular file containing the Details, which lists + and – strand information separately.  The start and end represent the lower and higher coordinates of the exclusion zone from GeneTrack, and “Value” is the tag count sum within the exclusion zone.  The peak pair midpoint is calculated along with the distance between the two paired peaks (midpoint-to-midpoint or C-W distance).

 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
 * **closest/largest/mode F** - pdf file that provides the final plots graph.
 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).

    </help>
    <expand macro="citations" />
</tool>