ChIP-Seq Top2 in Yeast - Revision history

Jw297: Protected "ChIP-Seq Top2 in Yeast" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))

2018-06-04T09:16:53Z

Protected "ChIP-Seq Top2 in Yeast" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))

2017-11-01T14:49:38Z

2017-10-09T22:10:55Z

2017-10-09T21:51:49Z

2017-10-09T21:31:31Z

2017-10-09T21:26:39Z

2017-10-09T16:39:46Z

2017-10-09T16:34:15Z

2017-10-09T16:19:59Z

2017-10-09T16:13:12Z

@@ Line 5: / Line 5: @@
 * [[ChIP-Seq Top2 peak-calling]]
 * [[ChIP-Seq Top2 peak-calling E2]]
 = Sample quality =

@@ Line 107: / Line 107: @@
 * NA_control_lambda.bdg, almost the same as the pileup file, but most probably refering to the INP. The meaning of word lambda is unclear here.
 ('''NA''' is the default prefix, another can be chosen)
 = Categorisation as peak =

@@ Line 104: / Line 104: @@
 * NA_summits.bed, more a summary of the previous file ... recording the max value for each of the peaks called.
 * NA_peaks.xls
-* NA_treat_pileup.bdg
+* NA_treat_pileup.bdg, a high resolution 4 column bedgraph file of the basic signal (floating point). Contiguous loci with same signal are grouped together. It is assumed that it refers to the IP signal.
-* NA_control_lambda.bdg
+* NA_control_lambda.bdg, almost the same as the pileup file, but most probably refering to the INP. The meaning of word lambda is unclear here.
 ('''NA''' is the default prefix, another can be chosen)
@@ Line 116: / Line 116: @@
 The source for this is from the MACS developer and is detailed [https://gist.github.com/taoliu/2469050 here].
 = Differential Peak-calling =

@@ Line 101: / Line 101: @@
 MACS automatically produces five files as output:
-* NA_control_lambda.bdg
+* NA_peaks.narrowPeak, a 6+4 bedgraph file with two of the four columns being p-values and q-value (false discovery rate). It's the principal peak-calling file.
-* NA_peaks.narrowPeak, a 6+4 bedgraph file with two of the four columns being p-values and q-value (false discovery rate).
+* NA_summits.bed, more a summary of the previous file ... recording the max value for each of the peaks called.
 * NA_peaks.xls
 * NA_treat_pileup.bdg
 ('''NA''' is the default prefix, another can be chosen)

← Older revision		Revision as of 21:26, 9 October 2017
Line 100:		Line 100:
	* the size of the genome is then given for the -g option.		* the size of the genome is then given for the -g option.

−	MACS produces ~~a number of~~ files as output.	+	MACS automatically produces five files as output:
		+	* NA_control_lambda.bdg
		+	* NA_peaks.narrowPeak, a 6+4 bedgraph file with two of the four columns being p-values and q-value (false discovery rate).
		+	* NA_peaks.xls
		+	* NA_summits.bed
		+	* NA_treat_pileup.bdg
		+	('''NA''' is the default prefix, another can be chosen)

← Older revision	Revision as of 09:16, 4 June 2018
(No difference)

@@ Line 96: / Line 96: @@
 * $BAM1 is the name of the immunoprecipitation alignment file, termed the '''treatment''' and therefore given with the '''-t''' option.
 * $BAM2 is the name of the normal input alignment file, termed the '''control''' and therefore given with the '''-c''' option.
-categories and Signal =
+MACS produces a number of files as output.
 It is not totally clear how MACS decides that a peak should be called. This is apparent when the signal appears to rise and fall, yet MACS does not call a peak.

@@ Line 88: / Line 88: @@
 * [http://stab.st-andrews.ac.uk/top2/bamfiltquals3/ULS1_T2_INP_srtd_filt3_bamqc.html ULS1_T2_INP_E2]
-= MACS Peak categories and Signal =
+= The MACS/2 program =
 It is not totally clear how MACS decides that a peak should be called. This is apparent when the signal appears to rise and fall, yet MACS does not call a peak.

← Older revision		Revision as of 16:19, 9 October 2017
Line 94:		Line 94:
	== Signal script ==		== Signal script ==

−	The source for this is from ~~teh~~ MACS developer and is detailed [https://gist.github.com/taoliu/2469050 here].	+	The source for this is from the MACS developer and is detailed [https://gist.github.com/taoliu/2469050 here].