ACT IntegratedSample - Revision history

Justin.jee: Replaced content with 'ACT Integrated Example: Whole-Genome ChIP-Seq experiments see http://info.gersteinlab.org/ACT_IntegratedExample'

2010-09-10T17:46:52Z

Replaced content with 'ACT Integrated Example: Whole-Genome ChIP-Seq experiments see http://info.gersteinlab.org/ACT_IntegratedExample'

← Older revision		Revision as of 17:46, 10 September 2010
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	ACT Integrated Example: Whole-Genome ChIP-Seq experiments		ACT Integrated Example: Whole-Genome ChIP-Seq experiments

	~~Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments.~~		see http://info.gersteinlab.org/ACT_IntegratedExample

	~~To begin, download the signal files (from Gerstein Lab's PeakSeq project) here:~~

	~~http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/PolII/Signal_Maps/PolII/~~

	http://~~archive~~.gersteinlab.org/~~proj/PeakSeq/Scoring_ChIPSeq/Results/STAT1/Signal_Maps/STAT1/~~

	These are zipped signal files for PolII and Stat1. After unzipping the files for each transcription factor, it is useful to cat the signal tracks for the individual chromosomes together so that all the signals are in only two files. In this walkthrough they will be referred to as PolII.sgr and Stat1.sgr.

	*Aggregation

	*Correlation

	~~It is necessary to convert the signal tracks from sgr to wig format. A script which does this can be found here:~~

	~~http://act.gersteinlab.org/sgr2wig.pl~~

	*Saturation

	It is necessary to convert the wig files to bed files without a "signal" component. The following script takes wig files and converts them into bed files, with coordinates representing the regions of the signal track which are above a certain threshold (in this case 0).

	~~http://act.gersteinlab.org/wig2bed.pl~~

	~~Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.~~

Justin.jee at 16:12, 6 September 2010

2010-09-06T16:12:56Z

← Older revision		Revision as of 16:12, 6 September 2010
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	*Correlation		*Correlation

			It is necessary to convert the signal tracks from sgr to wig format. A script which does this can be found here:

			http://act.gersteinlab.org/sgr2wig.pl

	*Saturation		*Saturation

			It is necessary to convert the wig files to bed files without a "signal" component. The following script takes wig files and converts them into bed files, with coordinates representing the regions of the signal track which are above a certain threshold (in this case 0).

			http://act.gersteinlab.org/wig2bed.pl

	Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.		Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.

Mbg at 12:42, 6 September 2010

2010-09-06T12:42:01Z

← Older revision		Revision as of 12:42, 6 September 2010
Line 1:		Line 1:
	ACT Integrated Example: Whole-Genome ChIP-Seq experiments		ACT Integrated Example: Whole-Genome ChIP-Seq experiments

	Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments. To begin, download the signal files (from Gerstein Lab's PeakSeq project) here:		Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments.

			To begin, download the signal files (from Gerstein Lab's PeakSeq project) here:

	http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/PolII/Signal_Maps/PolII/		http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/PolII/Signal_Maps/PolII/

	http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/STAT1/Signal_Maps/STAT1/		http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/STAT1/Signal_Maps/STAT1/

Justin.jee at 12:20, 6 September 2010

2010-09-06T12:20:58Z

← Older revision		Revision as of 12:20, 6 September 2010
Line 6:		Line 6:

	These are zipped signal files for PolII and Stat1. After unzipping the files for each transcription factor, it is useful to cat the signal tracks for the individual chromosomes together so that all the signals are in only two files. In this walkthrough they will be referred to as PolII.sgr and Stat1.sgr.		These are zipped signal files for PolII and Stat1. After unzipping the files for each transcription factor, it is useful to cat the signal tracks for the individual chromosomes together so that all the signals are in only two files. In this walkthrough they will be referred to as PolII.sgr and Stat1.sgr.

			*Aggregation

			*Correlation

			*Saturation

			Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.

Justin.jee: Created page with 'ACT Integrated Example: Whole-Genome ChIP-Seq experiments Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments. To begin, download the s…'

2010-09-05T15:45:04Z

Created page with 'ACT Integrated Example: Whole-Genome ChIP-Seq experiments Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments. To begin, download the s…'

New page

ACT Integrated Example: Whole-Genome ChIP-Seq experiments

Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments. To begin, download the signal files (from Gerstein Lab's PeakSeq project) here:
http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/PolII/Signal_Maps/PolII/
http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/STAT1/Signal_Maps/STAT1/

These are zipped signal files for PolII and Stat1. After unzipping the files for each transcription factor, it is useful to cat the signal tracks for the individual chromosomes together so that all the signals are in only two files. In this walkthrough they will be referred to as PolII.sgr and Stat1.sgr.