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Protocols

SeqBuster specifications

Information


Unique identifier OMICS_00367
Name SeqBuster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • miraligner

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Eulalia Martí
  • person_outline Xavier Estivill

Additional information


https://github.com/lpantano/seqbuster/wiki

Publications for SeqBuster

SeqBuster citations

 (21)
library_books

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk

2018
PLoS One
PMCID: 5837101
PMID: 29505615
DOI: 10.1371/journal.pone.0193527

[…] Sequences fulfilling QC were used as the input for the seqBuster/seqCluster tool that retrieves three matrices of counts: i) miRNA, ii) isomiRs, and iii) small RNA clusters [, ]. In order to detect miRNAs and isomiRs, reads were mapped to hairpins release […]

call_split

Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis

2018
Genetics
PMCID: 5887145
PMID: 29467169
DOI: 10.1534/genetics.118.300791
call_split See protocol

[…] w reads were collapsed based on sequence identity using the collapse_reads_md.pl module of mirdeep2. Collapsed reads were further annotated for miRNA by mapping to miRBase version 21 (; ; ) using the miraligner module of seqbuster (). IsomiRs were identified using the R isomiRs (v1.3.0) package of seqbuster. Pairwise differential expression was performed among different groups using DESEQ2 (v1.12. […]

call_split

Regional and subtype dependent miRNA signatures in sporadic Creutzfeldt Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis

2018
PLoS Pathog
PMCID: 5794191
PMID: 29357384
DOI: 10.1371/journal.ppat.1006802
call_split See protocol

[…] Reads were trimmed to 36 nt and ligation adapters were removed using the adrec.jar program from the seqBuster suite (http://github.com/lpantano/seqbuster) [] with the following options: java -jar adrec.jar 1 8 0.3. Sequences were mapped to the hg19 genome with the command line: bowtie -f -v 1 –a–bes […]

call_split

The dynamic recruitment of TRBP to neuronal membranes mediates dendritogenesis during development

2017
EMBO Rep
PMCID: 5835843
PMID: 29263199
DOI: 10.15252/embr.201744853
call_split See protocol

[…] ucleotides. The remaining reads were mapped to the rat mature miRNAs (miRBase v21) using default parameters (one mismatch, 3 nt in the 3′ or 5′‐trimming variants, 3 nt in the 3′‐addition variants) of Miraligner software . For mature miRNA analysis, only those that are represented by at least 10 reads per million (RPM) in one of the conditions were considered. Differential expression analysis of mi […]

library_books

Non coding RNA analysis in fibrolamellar hepatocellular carcinoma

2017
Oncotarget
PMCID: 5828204
PMID: 29535801
DOI: 10.18632/oncotarget.23325

[…] umina, San Diego, CA) following the manufacturer's protocol. Libraries were sequenced with 1 × 50 bp single-end reads on an Illumina HiSeq 2000 system. Small RNA reads were mapped and quantified with miraligner and quantified read counts were annotated with Gencode v19. Differential miRNA expression analysis was performed using R version 3.2.3 [] with the Bioconductor package DESeq2 [] incorporati […]

call_split

A comprehensive profile of circulating RNAs in human serum

2017
RNA Biol
PMCID: 5798962
PMID: 29219730
DOI: 10.1080/15476286.2017.1403003
call_split See protocol

[…] 9 (10 alignments per read were allowed). We compiled a comprehensive annotation set from miRBase/MirGeneDB [] for miRNAs, pirBAse/pirnabank for piRNAs [], GENCODE [] for other RNAs and tRNAs. We used SeqBuster [] to get isomiR and miRNA profiles of our samples. To count the reads mapped on other RNAs, HTSeq [] was utilized in a Python script. We used a threshold of 10 median read count per sncRNA […]

Citations

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SeqBuster institution(s)
Genetic Causes of Disease Group, Genes and Disease Program, Centre for Genomic Regulation (CRG), Barcelona, Spain; Centro de Investigacion Biomedica en Red en Epidemiologıa y Salud Publica (CIBERESP), Barcelona, Spain; Experimental and Health Sciences Department, Pompeu Fabra University, Barcelona, Catalonia, Spain
SeqBuster funding source(s)
Supported by Spanish Ministry of Health Fondo de Investigaciones Sanitarias (PI081367) and Instituto de Salud Carlos III (CIBERESP), Spanish Ministry of Science and Innovation (SAF2008-00357) the Sixth Framework Programme of the European Commission through the SIROCCO integrated project LSHG-CT-2006-037900, the Spanish Ministry of Science and Innovation (SAF2008-00357), the Spanish Ministry of Health and a fellowship from the Spanish Ministry of Science and Innovation MICINN.

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