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Unique identifier OMICS_02561
Name Illumina Data Sets
Restrictions to use None
Maintained Yes

Illumina Data Sets citations


Global gene expression reveals stress responsive genes in Aspergillus fumigatus mycelia

BMC Genomics
PMCID: 5715996
PMID: 29202712
DOI: 10.1186/s12864-017-4316-z

[…] Illumina data sets were trimmed using Trimmomatic (ver. 0.33), where sequencing adapters and sequences with low-quality scores were removed []. Cleaned reads were mapped to the genome sequence of A. f […]


Dense and accurate whole chromosome haplotyping of individual genomes

Nat Commun
PMCID: 5670131
PMID: 29101320
DOI: 10.1038/s41467-017-01389-4

[…] d numbers of single cells, we randomly selected subsets of either 5, 10, 20, 40, 60, 80, 100, or 120 libraries from the original number of 134 libraries in the data set. Read data from the PacBio and Illumina data sets were downsampled using Picard (picard-tools-1.130) to meet a defined depth of coverage of either 2, 3, 5, 10, 15, 25, or 30-fold. The downsampling was performed for five independent […]


Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

PMCID: 5649159
PMID: 28696422
DOI: 10.1038/ismej.2017.101

[…] is, the data were prepared as follows. Contigs longer than 20 000 bp were split into sub-contigs of at least 10 000 bp length with the provided script (). The non-normalized Illumina reads of the six Illumina data sets were mapped to the sub-contigs with bowtie2 v. 2.2.2 at default settings (). The resulting SAM files were converted to BAM, sorted and indexed with samtools v. 0.1.18 (), and duplic […]


Positional bias in variant calls against draft reference assemblies

BMC Genomics
PMCID: 5368935
PMID: 28351369
DOI: 10.1186/s12864-017-3637-2

[…] Arabidopsis thaliana (TAIR10) were downloaded from The Arabidopsis Information Resource website [].To simulate the reads we used SimSeq application that aims to reproduce the biases present in normal Illumina data sets []. We ran the application with default parameters to simulate 15 mln 100 bp paired-end reads with the mean insert size of 180 bp and 5 mln 100 bp mate-pair reads with the mean inse […]


Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA Seq

PLoS One
PMCID: 4954708
PMID: 27438485
DOI: 10.1371/journal.pone.0159407

[…] s did not match known protein families in the five public protein databases. Therefore, we consider them to represent unknown protein families, indicating that novel information was discovered in our Illumina data sets, in particular the 1,649 UniGenes without functional annotation among the DEGs. There were 49,230 UniGenes (88.8%) that comprise a group that did not show differential expression be […]


Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy

BMC Genomics
PMCID: 4869263
PMID: 27185182
DOI: 10.1186/s12864-016-2689-z

[…] Illumina data sets were trimmed using fastq-mcf in ea-utils (v1.1.2-484) [], where sequencing adapters and sequences with low-quality scores (Phred score Q < 20) were removed. Cleaned reads were mappe […]


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