Chimira specifications

Information


Unique identifier OMICS_09033
Name Chimira
Interface Web user interface
Restrictions to use None
Input data FASTQ/FASTA files
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Dimitrios M. Vitsios <>

Publication for Chimira

Chimira in publications

 (7)
PMCID: 5861728
PMID: 29581793
DOI: 10.1186/s13148-018-0469-0

[…] of 7.58 mbp. file conversions, filtering, and sorting as well as mapping (bowtie2) were done using “galaxy” [–], a platform for data intensive biomedical research (https://usegalaxy.org/), and “chimira” [], respectively., paraffin sections were deparaffinized. antigen retrieval was performed for 15 min in citrate buffer using a rice cooker, then slides were cooled down on ice for 20 min. […]

PMCID: 5767269
PMID: 29375285
DOI: 10.3389/fnins.2017.00731

[…] the illumina developed bcl2fastq pipeline. raw sequencing data was deposited at ncbi's gene expression omnibus (accession number gse105811). further qc testing of the raw data was completed using chimira, a web-based system used for mirna analysis from small rna-sequencing data (vitsios and enright, ). briefly, the 3′ adapter sequences were trimmed and the overall mirna reads counted. […]

PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] the regulation of the positive transcription elongation factor p-tefb []., many mirna processing pipelines have been established for utilizing hts data. the major pipelines include: oasis [], chimira [], mirge [], and tiger [], etc. several tools have also been developed to detect isomirs such as seqbuster [], isomirid [] and deanniso []. one trna detection tool, tdrmapper [], […]

PMCID: 5768236
PMID: 28792939
DOI: 10.1038/nature23318

[…] mirna counts were identified from the small rna-seq input samples, cleaned from their 3’ adapters and mapped against all mouse hairpin precursors of the mirbase, allowing up to two mismatches using chimira,. counts of multi-mapped reads were assigned only to the first optimal alignment call returned by blastn. modification analysis was then restricted to pure modification events, i.e. mono-[nt] […]

PMCID: 5386655
PMID: 27935865
DOI: 10.18632/oncotarget.13806

[…] sequences from raw data for mirna-seq reads. then fastqc was used again to recheck the quality of the preprocessed reads. the mapping of the trimmed high quality mirna-seq reads was performed using chimira [], which is a fast and robust system for the cleaning, filtering, quality control, and mapping of mirna-seq data. the initially mapped mirna-seq reads were further adjusted […]


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Chimira institution(s)
EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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