TagDust protocols

TagDust specifications

Information


Unique identifier OMICS_01095
Name TagDust
Alternative name TagDust2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.33
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Timo Lassmann <>

Publications for TagDust

TagDust IN pipelines

 (10)
2018
PMCID: 5930951
PMID: 29716548
DOI: 10.1186/s12864-018-4692-z

[…] was sequenced on an illumina miseq (4 million reads generated per library). the sequencing data was analyzed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), filtered using tagdust2 [68], mapped using bwa [69], clustered using paraclu [70], and visualized using bedtools [71] and the ucsc genome browser [23]., rsox-4 was lr cloned upstream of a lacz reporter gene […]

2016
PMCID: 4821887
PMID: 27029645
DOI: 10.1038/ncomms11173

[…] kit at the unc high throughput sequencing facility. pools of 24 multiplexed samples were sequenced per lane on an illumina hiseq 2500 using 50-bp paired-end reads., rna-seq reads were filtered using tagdust and aligned to the reference mouse genome (mm9) with tophat using default parameters5960. reads aligning to ribosomal rna genes were removed. transcript abundance was estimated by computing […]

2016
PMCID: 4883752
PMID: 27231886
DOI: 10.1371/journal.pone.0156439

[…] kit at the unc high throughput sequencing facility. pools of 24 multiplexed samples were sequenced per lane in a hiseq 2500 sequencer using 50 bp paired-end reads., rna-seq reads were filtered using tagdust and aligned to the reference mouse genome (mm9) with tophat using default parameters. reads aligning to rrna genes were removed. transcript abundance was estimated by computing rpkm using […]

2016
PMCID: 5052795
PMID: 27677335
DOI: 10.1038/ncomms12983

[…] nested primer pair. outer and nested primers used in this study are presented in supplementary tables 4 and 5 respectively., primer sequences at the 5′ ends of sequencing reads were trimmed using tagdust2, and mapped to the reference genome (hg19) using bowtie2 (2.2.6). unaligned reads were trimmed at the first 50 base pairs before realigning them to the reference genome. only uniquely mapped […]

2015
PMCID: 4346264
PMID: 25730316
DOI: 10.1371/journal.pone.0118631

[…] were run at the same time. these sequence analyses were carried out by riken genas (yokohama, japan)., after base calling, we removed linker sequences and artificial linker adapter sequences using tagdust v1.13 [40], and identified the reads matching the ribosomal dna repeating unit (genbank accession number u13369) within two mismatches. only the remaining reads were mapped to the human […]

TagDust institution(s)
RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Institute, Yokohama, Japan; Telethon Kids Institute, The University of Western Australia, Subiaco, WA, Australia
TagDust funding source(s)
Supported by a Research Grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to the RIKEN Center for Life Science Technologies.

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