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Showing content from https://github.com/GuanLab/Anchor below:

GuanLab/Anchor: This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge

Anchor: Trans-cell Type Prediction of Transcription Factor Binding Sites

This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge

background: ENCODE-DREAM

Please contact (gyuanfan@umich.edu or hyangl@umich.edu) if you have any questions or suggestions.

The paper is published in Genome Research: Li H, Quang D, Guan Y. 2019. Anchor: Trans-cell Type Prediction of Transcription Factor Binding Sites. Genome Research. 2019 Feb;29(2):281-292. doi: 10.1101/gr.237156.118. Epub 2018 Dec 19.

Git clone a copy of ANCHOR:

git clone https://github.com/GuanLab/Anchor.git

perl (5.10.1)
python (3.6.5)
numpy (1.13.3) It comes pre-packaged in Anaconda.
opencv (3.4.2)
samtools (1.1)
bigWigToBedGraph
xgboost

Required input files (and the corresponding directories to put them)

Genomic coordinates

./data/ref/ genomic coordinates under consideration (e.g. test_regions.blacklistfiltered.bed)

DNase-seq data (e.g. H1-hESC)

./data/dnase_aln/ read alignemnt BAM file (one or multiple replicates)
./data/dnase_fold_coverage/ fold-enrichement signal coverage tracks Bigwig file

DNA sequence and motif

./data/hg_genome/ human genome sequence
./data/motif/ TF motifs (e.g. motif)

Gencode

./data/ref/gencode.v19.annotation.gtf
It can be downloaded from this here:

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz

Prepare features and make predictions

Once the required input files are put in the correpsonding directories, ANCHOR is ready to go:

python ANCHOR.py -tf TAF1 -cell H1-hESC

The prediction results are saved here:

./prediction/anchor/final/

This is the one-line-to-run version. The implemetation details of feature generation and binding site prediction (with step-by-step explanation and example code) can be found here: DETAILS

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