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FStitch specifications

Information


Unique identifier OMICS_10575
Name FStitch
Alternative name Fast Read Stitcher
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data FStitch requires a BedGraph file.
Operating system Unix/Linux
Programming languages C++
Parallelization OpenMP
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Joseph Azofeifa <>

Publication for Fast Read Stitcher

FStitch in publications

 (2)
PMCID: 5829637
PMID: 29240919
DOI: 10.1093/nar/gkx1225

[…] using macs2 version 2.1.0.20150731 () under default settings and a p-value cutoff of 1e–05. we used –broad -g hs –keep-dup = auto -p 1e-5 -m 10 200 –bw 200 and selected broad peak calls., the fstitch algorithm () was used to identify genomic regions enriched with h3k9ac and –k27ac signal from hct116 chip-seq experiments. in order to acquire uniform fstitch signal calls across experiments […]

PMCID: 5942361
PMID: 27663494
DOI: 10.1093/bioinformatics/btw599

[…] our model on publicly available biological data. to perform model inference of rnap location requires an interval [a,b] where gro-seq read mapping data (d) can be collected. to this end, we utilized fast read stitcher (fstitch) that implements a maximum entropy markov model to segment the genome into ‘transcribed regions’ (, ). in a hct116 gro-seq dataset (), fstitch classified 19 709 […]


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FStitch institution(s)
University of Colorado, Boulder, CO, USA

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