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phantompeakqualtools

Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays. Phantompeakqualtools can be used to (i) Compute the predominant insert-size (fragment length) based on strand cross-correlation peak; (ii) compute data quality measures based on relative phantom peak; (iii) call peaks and regions for punctate binding datasets

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1 user review

1 user review

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

Indispensable for ChIP-seq and ATAC-seq quality control. Produces a graph showing the crosscorrelation of reads distributions on forward and reverse strand as well as ratios to estimate the noise. Be carefull however, because these ratios are meaningfull only for narrow peaks, not for broad peaks like H3K27me3 or H3K36me3.

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phantompeakqualtools classification

phantompeakqualtools specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
BED
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input format:
BAM, BED
Operating system:
Unix/Linux
License:
MIT License
Version:
1.1
Maintained:
Yes

phantompeakqualtools distribution

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phantompeakqualtools support

Documentation

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