Eoulsan protocols

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Eoulsan specifications

Information


Unique identifier OMICS_01402
Name Eoulsan
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Parallelization MapReduce
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Publication for Eoulsan

Eoulsan in pipelines

 (5)
2017
PMCID: 5368712
PMID: 28377822
DOI: 10.1038/celldisc.2017.5

[…] on a hiseq 1500 device (illumina, san diego, ca, usa). a mean of 72±17 million passing illumina quality filter reads was obtained for each of the nine samples., analyses were performed using the eoulsan pipeline [], including read filtering, mapping, alignment filtering, read quantification. before mapping, reads ⩽40 bases were removed, and reads with quality mean ⩽30 were discarded. reads […]

2017
PMCID: 5588705
PMID: 28912831
DOI: 10.1186/s13068-017-0897-7

[…] paired-end read sequencing on a hiseq 1500 device. a mean of 52 ± 10 million passing illumina quality filter reads was obtained for each of all the samples. we performed rna-seq analysis using the eoulsan pipeline []. only read 1 was considered for the further analyses. before mapping, poly n read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. […]

2015
PMCID: 4313713
PMID: 25698924
DOI: 10.3389/fncel.2015.00009

[…] (bp) single read sequencing on a hiseq 2000 device. a mean of 56 ± 27 million passing illumina quality filter reads was obtained for each samples., the whole rna-seq data analysis was done using the eoulsan software version 1.1.6 (jourdren et al., ) with the following parameters. before mapping, polyn read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 […]

2014
PMCID: 4279801
PMID: 25550711
DOI: 10.1186/s13068-014-0173-z

[…] on a hiseq 2000 device. a mean of 53 ± 12 million passing illumina quality filter reads was obtained for each of the two samples’ rna-seq data analysis., we performed rna-seq analysis using the eoulsan pipeline []. before mapping, poly n read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. reads were then aligned against the t. reesei genome […]

2013
PMCID: 3734080
PMID: 23897886
DOI: 10.1083/jcb.201305041

[…] reference genome (bowtie 0.12.9). alignments were filtered to avoid nonaligned reads and multiple alignments reads (picard, samtools). abundance was estimated at gene level using htseq-count 0.5.3, eoulsan version ()., sds-page was performed using standard protocols. proteins were transferred to nitrocellulose membranes (emd millipore) and detected with antibodies. membranes were incubated […]


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Eoulsan in publications

 (6)
PMCID: 5924386
PMID: 29565275
DOI: 10.3390/brainsci8040050

[…] (illumina, san diego, ca, usa). a mean of 50 ± 18 million passing illumina quality filter reads was obtained for each sample., rnaseq bioinformatics analysis: analyses were performed using the eoulsan pipeline version 2.0-alpha5 [], including read filtering, mapping, alignment filtering, read quantification. before mapping, reads ≤40 bases were removed, and reads with quality mean ≤30 […]

PMCID: 5859163
PMID: 29556065
DOI: 10.1038/s41598-018-23106-x

[…] models by adapting the methodology applied in and. estimation of expression (normalized deseq counts) and differential gene expression analysis at different stages of the study was performed using eoulsan, using parameters as indicated in eoulsan parameter file used, (file s3). statistical analysis to compare the expression of genes was performed using two-sample t-test with unequal variance., […]

PMCID: 5549768
PMID: 28749941
DOI: 10.1371/journal.pgen.1006903

[…] hiseq system (e9.5 embryos) or using 42 bp paired-end reads on an illumina nextseq (e8.5 embryos) according to the manufacturer’s specifications. chip-seq data were analysed as follows, using eoulsan [] with extended support for chip-seq workflows (https://github.com/genomicpariscentre/eoulsan/tree/branch-chip-seq). first, reads were filtered out when they would not pass illumina filters […]

PMCID: 4812632
PMID: 27030800
DOI: 10.1186/s13068-016-0488-z

[…] that exhibited an sd >20 % of the mean value within replicates, false discovery rates ([] were used to assess the significance of values. data from rna deep sequencing were analysed using the eoulsan software version 1.2.2 []. to quantify the gene expression level, the relative transcript abundance was measured in reads per kb of exon per million mapped sequence reads (rpkm; []). […]

PMCID: 4390390
PMID: 25626518
DOI: 10.1111/mmi.12944

[…] for each of the 12 samples. transcriptomic analysis was performed as three experimental replicates from which mean values were calculated and presented. rna-seq data analysis was done using the eoulsan software version 1.2.2 (jourdren et al., ). before mapping, poly n read tails were trimmed, reads ≤ 40 bases were removed, and reads with quality mean ≤ 30 were discarded. reads […]


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Eoulsan institution(s)
École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France; Inserm, U1024, Paris, France; CNRS, UMR 8197, Paris, France; Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
Eoulsan funding source(s)
Supported by the network Infrastructures en Biologie Santé et Agronomie (IBiSA) and by an Amazon Web Services research grant.

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