SWEMBL statistics

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SWEMBL specifications


Unique identifier OMICS_18253
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED
Output format ELAND
Operating system Unix/Linux
Programming languages C
License Apache License version 2.0
Computer skills Advanced
Version 3.6
Stability Stable
Maintained Yes



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  • person_outline Steven Wilder <>

SWEMBL in pipeline

PMCID: 4359374
PMID: 25279814
DOI: 10.7554/eLife.02626.031

[…] their respective genomes () (). sequence reads from high quality replicates were pooled prior to calling peaks used for all comparative analyses and building crms. peak calling was performed using swembl with parameters ‘-r 0.005 -i –s’ as described previously (http//www.ebi.ac.uk/∼swilder/swembl/; ). the correlation of normalized read counts between biological replicates in the chip-seq data […]

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SWEMBL in publications

PMCID: 5741965
PMID: 29272997
DOI: 10.1186/s12864-017-4351-9

[…] replicates for each species/strain and for three liver-specific transcription factors (cebpa, hnf4a and foxa1). reads were aligned using bwa [] with default parameters. peak locations were called by swembl (https://github.com/stevenwilder/swembl). final peak sets contained peaks present in both biological replicates., we compared peaks generated from chip-seq datasets among the five mouse […]

PMCID: 5354662
PMID: 28055971
DOI: 10.18632/oncotarget.14401

[…] androgen stimulated and src condition, but not the vehicle-treated condition, were analyzed further. enriched regions of the genome were identified by comparing chip samples to input samples using swembl peak caller version 3.2 (http://www.ebi.ac.uk/∼swilder/swembl/), macs and chipseqmini. only peaks that were present in >2 samples in each treatment group, and peaks that were identified […]

PMCID: 5006368
PMID: 27582050
DOI: 10.1186/s13059-016-1043-8

[…] to keep duplicated reads. for histone modifications and rna polymerase ii binding, peaks were called with additional “—broad –broad-cutoff 0.05” options. to compare chip-seq and chip-exo peaks, the swembl (www.ebi.ac.uk/~swilder/swembl) peak caller was used with parameter “-r 0.005.”, the genomic distribution of top2b binding was annotated using the cis-regulatory element annotation system […]

PMCID: 4868113
PMID: 26882985
DOI: 10.1093/molbev/msw030

[…] with default parameters. numbers of mapped reads and quality metrics are shown in supplementary table s2, supplementary material online, for the liver-enriched tfs. peak calling was performed with swembl (v3.3.1; https://www.ebi.ac.uk/∼swilder/swembl/) with the parameter “-r 0.005.” tf peaks were called as reproducible in both replicates if they overlapped by  ≥75% reciprocally (supplementary […]

PMCID: 3923681
PMID: 24550742
DOI: 10.1371/journal.pgen.1004153

[…] bowtie alignment software, with the following parameters: bowtie -m 1 -s -k 1 –n 1. unique reads were selected for further analysis., peak calling for the chip sequencing data was performed with swembl (url: http://www.ebi.ac.uk/~swilder/swembl/) as described with the respective parameters described in ., co-localization read density profiles were done by extending a region around each peak […]

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