ChIP-seq Analysis - Revision history

Semyonk@dote.ru at 08:52, 3 May 2019

2019-05-03T08:52:07Z

2019-03-25T09:42:39Z

2019-03-25T09:38:34Z

2019-03-25T09:38:03Z

2019-03-25T09:21:21Z

2019-03-25T09:17:09Z

2019-03-25T09:10:53Z

2019-03-25T09:10:31Z

2019-03-20T12:32:31Z

‎Description

2019-03-20T05:36:58Z

@@ Line 2: / Line 2: @@
 Processing raw ChIP-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
 === Use case ===
-[https://www.youtube.com/watch?v=JTVbHIzm8HI ChIP-seq FPCM and FNCM Quality Analysis use case]
+[https://youtu.be/ylnus1SSS_w ChIP-seq FPCM and FNCM Quality Analysis use case]
 ==== FPCM and FNCM ====
 To determine FPCM (False Positive Control Metric) and FNCM (False Negative Control Metric), it is necessary initially to merge  all given datasets of Transcription Factor Binding Regions (TFBRs). FPCM is determined the ratio of observed number f of orphans to the expected number of genuine orphans f<sub>e</sub> , i.e.

@@ Line 2: / Line 2: @@
 Processing raw ChIP-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
 === Use case ===
-{{YouTube|id=JTVbHIzm8HI|title=ChIP-seq FPCM and FNCM Quality Analysis use case}}
+[https://www.youtube.com/watch?v=JTVbHIzm8HI ChIP-seq FPCM and FNCM Quality Analysis use case]
 ==== FPCM and FNCM ====
 To determine FPCM (False Positive Control Metric) and FNCM (False Negative Control Metric), it is necessary initially to merge  all given datasets of Transcription Factor Binding Regions (TFBRs). FPCM is determined the ratio of observed number f of orphans to the expected number of genuine orphans f<sub>e</sub> , i.e.

@@ Line 2: / Line 2: @@
 Processing raw ChIP-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
 === Use case ===
 {{YouTube|id=JTVbHIzm8HI|title=ChIP-seq FPCM and FNCM Quality Analysis use case}}
 ==== FPCM and FNCM ====

@@ Line 2: / Line 2: @@
 Processing raw ChIP-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
 === Use case ===
-[[File:Example.mp4|thumb|thumbtime=1:58|right|1280px|Tutorial video for 'Video on Wikipedia' (''how very meta!'')]]
+<iframe width="560" height="315" src="https://www.youtube.com/embed/JTVbHIzm8HI" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 ==== FPCM and FNCM ====
 To determine FPCM (False Positive Control Metric) and FNCM (False Negative Control Metric), it is necessary initially to merge  all given datasets of Transcription Factor Binding Regions (TFBRs). FPCM is determined the ratio of observed number f of orphans to the expected number of genuine orphans f<sub>e</sub> , i.e.

@@ Line 2: / Line 2: @@
 Processing raw ChIP-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
 === Use case ===
-<html5media height="720" width="1280">File:Example.mp4</html5media>
+[[File:Example.mp4|thumb|thumbtime=1:58|right|1280px|Tutorial video for 'Video on Wikipedia' (''how very meta!'')]]
 ==== FPCM and FNCM ====
 To determine FPCM (False Positive Control Metric) and FNCM (False Negative Control Metric), it is necessary initially to merge  all given datasets of Transcription Factor Binding Regions (TFBRs). FPCM is determined the ratio of observed number f of orphans to the expected number of genuine orphans f<sub>e</sub> , i.e.

@@ Line 1: / Line 1: @@
 === Description ===
-Processing raw Chip-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
+Processing raw ChIP-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications
 ==== FPCM and FNCM ====

@@ Line 26: / Line 26: @@
 * '''Select BED-files''' – Select BED-files
 '''FPCM and FNCM Estimation Parameters'''
-* '''Minimal length of binding region''' – Binding regions shorter than the minimal length would be extended
+* '''Minimal length of binding region''' – Binding regions shorter than the minimal length will be extended
-* '''Maximal length of binding region''' – Binding regions longer than the minimal length would be narrowed
+* '''Maximal length of binding region''' – Binding regions longer than the minimal length will be narrowed
 * '''FPCM threshold''' – If the FPCM exceeds the threshold, the FNCM will be calculated based on Chapman’s estimate
 * '''Calculate AUC?''' – Calculate AUC?