GTRD Workflow - Revision history

Fkolpakov@gmail.com at 10:59, 29 November 2017

2017-11-29T10:59:42Z

2016-10-10T08:18:07Z

‎Metaclusters

2016-10-10T08:17:18Z

2016-10-10T08:11:51Z

2016-10-10T06:21:39Z

2016-07-01T10:24:12Z

2016-07-01T10:23:06Z

2016-07-01T10:21:26Z

2016-07-01T10:20:22Z

2016-07-01T10:19:01Z

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 Clusters for the same TF revealed by different peak calling methods were joined into metaclusters. Metaclusters represent non-redundant set of transcription factor binding sites.
 ==Bowtie2==
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 [[File: gtrd-workflow-pics-script.png]]
 ==Clusters==

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 ==Metaclusters==
-Clusters for the same transcription factor revealed by different peak calling methods were joined into metaclusters. Cluster centers located 50 bp from each other or closer were grouped, and one of them was selected based on priority of peak caller. Peak callers from high priority to low prioruty: GEM, PICS, MACS, SISSRs. Metaclusters supported by only one peak caller were filtered out. Metaclusters represent non-redundant set of transcription factor binding sites.
+Clusters for the same transcription factor revealed by different peak calling methods were joined into metaclusters. Cluster centers located 50 bp from each other or closer were grouped, and one of them was selected based on priority of peak caller. Peak callers from high priority to low priority: GEM, PICS, MACS, SISSRs. Metaclusters supported by only one peak caller were filtered out. Metaclusters represent non-redundant set of transcription factor binding sites.
 ==References==
 <references />

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 As an estimate of the actual length, the length of the position weight matrix (PWM) for the corresponding transcription factor available from the [http://hocomoco.autosome.ru HOCOMOCO database] was used. When such an estimate was not available, we used the fixed length of 20 bp. The uncertainty in the location of cluster was estimated from the variation of peak centers inside that cluster. Specifically, we have computed the standard deviation (SD) of peak centers inside each cluster and used 4*SD as the uncertainty factor. When a cluster was supported by only a single peak, the median of SD values from all other clusters was used instead of SD. The width of cluster was computed as a sum of actual length and uncertainty factor.
 ==References==
 <references />

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 [[File: gtrd-workflow-pics-script.png]]
 ==References==
 <references />

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 [https://groups.csail.mit.edu/cgs/gem/ GEM] <ref> Yuchun Guo, Shaun Mahony & David K Gifford. High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints. PLoS Computational Biology 8(8): e1002638. 2012.</ref>
 and [http://www.bioconductor.org/packages/release/bioc/html/PICS.html PICS] <ref>Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S and Gottardo R. “PICS: Probabilistic Inference for ChIP-seq.” Biometrics, 66.  2010.</ref>.
 ==Bowtie2==

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 Raw ChIP-seq data in the form of fastq and SRA files were fetched from [http://genome.ucsc.edu/ENCODE/ ENCODE] and [http://www.ncbi.nlm.nih.gov/sra SRA] databases.
-Sequenced reads were aligned using [http://bowtie-bio.sourceforge.net/bowtie2 Bowtie2] aligner.
+Sequenced reads were aligned using [http://bowtie-bio.sourceforge.net/bowtie2 Bowtie2] <ref>Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.</ref> aligner.
 ChIP-seq peaks were called using 4 different methods:

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 Sequenced reads were aligned using [http://bowtie-bio.sourceforge.net/bowtie2 Bowtie2] aligner.
-ChIP-seq peaks were called using 4 different methods: [http://liulab.dfci.harvard.edu/MACS/ MACS] [http://sissrs.rajajothi.com/ SISSRS] [https://groups.csail.mit.edu/cgs/gem/ GEM] and [http://www.bioconductor.org/packages/release/bioc/html/PICS.html PICS].
+ChIP-seq peaks were called using 4 different methods:
 ==Bowtie2==
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 ==PICS==
-We use following R script to call peaks using PICS:
+For peak calling with PICS method we use R version 3.2.0 and PICS version 2.12.0.
 [[File: gtrd-workflow-pics-script.png]]