Partek Flow protocols

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chevron_left Differential expression Bioinformatics workflows Read quality control Known transcript quantification Spliced read alignment Gene expression visualization chevron_right
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Partek Flow specifications

Information


Unique identifier OMICS_15740
Name Partek Flow
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

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Partek Flow in pipelines

 (7)
2017
PMCID: 5321275
PMID: 28225783
DOI: 10.1371/journal.pone.0171471

[…] san diego, ca), 5% phix was spiked in. finally, a paired-end 301bp sequencing run was performed on the illumina miseq system (illumina, san diego, ca)., sequence analysis was performed using the partek flow software (partek inc. st. louis, mo, usa). adaptors and bases with phred quality scores <30 were trimmed from both ends and reads less than 25bp were removed. the remaining reads […]

2017
PMCID: 5423697
PMID: 28486541
DOI: 10.1371/journal.pone.0177245

[…] image analysis and base calling was carried out using rta 1.13.48.0. final file formatting, demultiplexing and fastq generation were carried out using casava v 1.8.2., rna-seq data was analyzed with partek flow version 4 (partek inc., st. louis, mo). raw sequencing reads were first trimmed from both ends with quality score method (bases with quality score phred less than 20 were trimmed […]

2017
PMCID: 5516996
PMID: 28723918
DOI: 10.1371/journal.pone.0180873

[…] alignment was performed to version mm10 of the mouse genome and annotated to refseq (5-2-16) using the bowtie2 algorithm within the tophat application., the aligned bam files were downloaded into partek flow and genomics suite (st louis, mo) for downstream analysis. the data summarization, quantification, and normalization of rna counts into total reads per kilobase of gene model per million […]

2017
PMCID: 5516996
PMID: 28723918
DOI: 10.1371/journal.pone.0180873

[…] contrast of interest was performed based on the gene ontology (go) and kegg (kyoto encyclopedia of genes and genomes) annotation using partek pathway. we also transferred the normalized data from partek flow into partek genomics suite to perform pathway anova using the kegg annotation database. this procedure tests for shifts in the expression of all of the transcripts represented […]

2016
PMCID: 5121338
PMID: 27869122
DOI: 10.1038/ncomms13362

[…] v2 (life technologies) and sequenced on the ion proton sequencer platform. raw sequence data were aligned to the latest draft of the human genome using the tophat2 and bowtie2 algorithms within the partek flow suite. using partek's gene specific analysis feature, we calculated enrichment or depletion of polyribosome-associated mrna in each fraction relative to total cellular mrna. […]


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Partek Flow in publications

 (40)
PMCID: 5918994
PMID: 29694377
DOI: 10.1371/journal.pone.0196058

[…] and the author of this manuscript has the following competing interests: nik tuzov holds full time, paid employment at partek incorporated. the commercial software produced by partek incorporated (“partek flow” and “partek genomics suite”) was used extensively to obtain the results presented in the manuscript. this affiliation does not alter the author’s adherence to plos one policies […]

PMCID: 5917821
PMID: 29534157
DOI: 10.1093/brain/awy057

[…] bc chip and sequenced on the ion proton system by ion pi ic 200 kit chemistry (200-bp read length; life technologies). the ion proton reads (fastq files) were imported into the rna-seq pipeline of partek flow software (v 4.0, partek inc), with hg19 as the reference genome. we identified genes differentially expressed between groups, by quantifying mapped reads with the partek e/m algorithm […]

PMCID: 5838106
PMID: 29507358
DOI: 10.1038/s41598-018-22409-3

[…] sequencing. libraries were constructed using truseq stranded mrna library prepkits (illumina, san diego, ca) and run on a hiseq. 2500 instrument (illumina). raw data were analyzed using partek flow and partek genomics suite software v6.0.17.0319 to determine transcript abundance and differentially expressed genes between samples. gene ontology analysis was performed using the gene […]

PMCID: 5747455
PMID: 29287116
DOI: 10.1371/journal.pone.0190445

[…] by using expression console software (affymetrix) to obtain raw data (cel files) and metrics for quality control. no apparent outliers were detected., specific mirna analysis involved use of partek flow v3.0 (partek inc., st. louis, mo). cel files were imported and normalized by robust multi-array averaging (rma). the mirna 4.0 chip contained probes for 490 rat pre-mirnas and 728 rat […]

PMCID: 5750478
PMID: 29244788
DOI: 10.1038/emm.2017.226

[…] cdna were assessed using a 2100 bioanalyzer (agilent technologies, santa clara, ca, usa). rna sequencing data are deposited at ncbi under accession code gse83990., rna-seq data were analyzed with partek flow version 4 (partek). raw sequencing reads were first trimmed from both ends with a quality score method (bases with a quality score of less than 20 were trimmed from both ends, and trimmed […]


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