Merging CAGE experiments - Revision history

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T06:08:59Z

‎Results on rn6 data

Ivan@dote.ru: /* Algorithm overview */

2021-03-05T06:05:52Z

‎Algorithm overview

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T06:04:05Z

‎Results on rn6 data

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T06:01:46Z

‎Results on rn6 data

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T06:01:05Z

‎Results on rn6 data

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T05:52:38Z

‎Results on rn6 data

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T05:52:08Z

‎Results on rn6 data

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T05:46:12Z

‎Results on rn6 data

Ivan@dote.ru at 05:42, 5 March 2021

2021-03-05T05:42:50Z

Ivan@dote.ru: /* Results on rn6 data */

2021-03-05T05:42:22Z

‎Results on rn6 data

@@ Line 77: / Line 77: @@
 At the last stage, adjacent segments that should be included in the NewReference are combined into one.
-===Results on rn6 data===
+===Results on rn6 and hg38 data===
 This method of combining CAGE data was applied to combine the FANTOM5 and UEXP data from Rattus norvegicus, as well as to combine the HumanMuscle and RefTSS data, resulting in the identification of new TSS and refining the boundaries of the previously known TSS. Detailed statistics are given in Tables 1 and 2.

@@ Line 49: / Line 49: @@
 A preliminary analysis of the rat CAGE data (Reference = FANTOM5, NewData = UEXP) showed a significant length of the overhangs (the average overhang length is 55% of the peak length for FANTOM5 peaks and 12% for UEXP peaks) as well as a significant proportion of multiple intersections (7.5% FANTOM5 peaks intersect with more than one UEXP peak and 1.1% of UEXP peaks intersect with more than one FANTOM5 peak).
-The presence of overhangs and multiple intersections can be caused both by the actual TSS activity in these regions in only one of the datasets or by the insufficient accuracy of determining the boundaries with the peak-caller due to insufficient coverage by reads. It is important to be able to distinguish between these cases, since in the first case this area should be included in the NewReference and in the second should not.
+The presence of overhangs and multiple intersections can be caused both by the actual TSS activity in these regions in only one of the datasets or by the insufficient accuracy of determining the boundaries with the peak-caller due to insufficient coverage by reads. It is important to be able to distinguish between these cases, since in the first case this region should be included in the NewReference and in the second should not.
 This requires an analysis of the read density profile in these regions. To do this, the entire genome is divided into segments defined by the boundaries of the peaks of both datasets (Fig. 5).
@@ Line 75: / Line 75: @@
 To compare the density of reads in segments, a binomial test is used, where p is the ratio of the length of the first segment to the sum of the lengths of the segments, n is the sum of the number of reads in the segments, k is the number of reads in the first segment. If p-value <= 0.01, then it is considered that the density is significantly less and the segment is discarded.
 At the last stage, adjacent segments that should be included in the NewReference are combined into one.
 ===Results on rn6 data===

@@ Line 113: / Line 113: @@
 {| class="wikitable" style="float:right; margin-left: 10px;"
-|+ style="text-align: left;" | Table 1. Homo sapiens CAGE datasets statistics.
+|+ style="text-align: left;" | Table 2. Homo sapiens CAGE datasets statistics.
+!
 ! Number of peaks

@@ Line 127: / Line 127: @@
 |-
 | Combined
-| 3986664
+| 242109
 | 3987kb
 |}

← Older revision		Revision as of 06:01, 5 March 2021
Line 108:		Line 108:
	* Joined peaks: 135		* Joined peaks: 135
	* Unchanged peaks: 18844		* Unchanged peaks: 18844
		+
		+
		+
		+
		+	{\| class="wikitable" style="float:right; margin-left: 10px;"
		+	\|+ style="text-align: left;" \| Table 1. Homo sapiens CAGE datasets statistics.
		+	!
		+	! Number of peaks
		+	! Bases count
		+	\|-
		+	\| REFTSS(hg38)
		+	\| 224694
		+	\| 4315kb
		+	\|-
		+	\| HumanMuscle
		+	\| 41767
		+	\| 536kb
		+	\|-
		+	\| Combined
		+	\| 3986664
		+	\| 3987kb
		+	\|}
		+	Summary of changes made to REFTSS(human) when combining with HumanMuscle dataset:
		+	* Changed peaks: 14061
		+	* Deleted peaks: 0
		+	* New peaks: 10407
		+	* Splitted peaks: 13109
		+	* Joined peaks: 365
		+	* Unchanged peaks: 204167

← Older revision		Revision as of 05:52, 5 March 2021
Line 79:		Line 79:

	===Results on rn6 data===		===Results on rn6 data===
−	This method of combining CAGE data was applied to combine the FANTOM5 and UEXP ~~rat~~ data, as well as to combine the HumanMuscle and RefTSS data, resulting in the identification of new TSS and refining the boundaries of the previously known TSS. Detailed statistics are given in Tables 1 and 2.	+	This method of combining CAGE data was applied to combine the FANTOM5 and UEXP data from Rattus norvegicus, as well as to combine the HumanMuscle and RefTSS data, resulting in the identification of new TSS and refining the boundaries of the previously known TSS. Detailed statistics are given in Tables 1 and 2.

@@ Line 82: / Line 82: @@
-''Table 1''
-{| class="wikitable"
+{| class="wikitable" style="float:right; margin-left: 10px;"
+!
 ! Number of peaks
@@ Line 100: / Line 101: @@
 | 644kb
 |}
 Summary of changes made to FANTOM5(rn6) when combining with UEXP data:
 * Changed peaks: 8058

← Older revision		Revision as of 05:46, 5 March 2021
Line 100:		Line 100:
	\| 644kb		\| 644kb
	\|}		\|}
		+
		+
		+	Summary of changes made to FANTOM5(rn6) when combining with UEXP data:
		+	* Changed peaks: 8058
		+	* Deleted peaks: 0
		+	* New peaks: 19017
		+	* Splitted peaks: 2805
		+	* Joined peaks: 135
		+	* Unchanged peaks: 18844

← Older revision		Revision as of 05:42, 5 March 2021
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	\| 644kb		\| 644kb
	\|}		\|}
−
−	~~===Further directions===~~
−	~~[[File:CAGE_merging_closely_spaced_peaks.png\|Closely spaced peaks]]~~

@@ Line 80: / Line 80: @@
 ===Results on rn6 data===
 This method of combining CAGE data was applied to combine the FANTOM5 and UEXP rat data, as well as to combine the HumanMuscle and RefTSS data, resulting in the identification of new TSS and refining the boundaries of the previously known TSS. Detailed statistics are given in Tables 1 and 2.
 ===Further directions===
 [[File:CAGE_merging_closely_spaced_peaks.png|Closely spaced peaks]]