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Basepair

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New York, New York, US

About Basepair

Basepair is a web-based, next-gen sequencing (NGS) data analytics company dedicated to accelerating the scientific discovery. We bring together the latest technologies in cloud computing, workflow automation, and interactive visualization to NGS data analysis without requiring costly investments in. Our... Show more »

Basepair is a web-based, next-gen sequencing (NGS) data analytics company dedicated to accelerating the scientific discovery. We bring together the latest technologies in cloud computing, workflow automation, and interactive visualization to NGS data analysis without requiring costly investments in. Our customers include leading academic institutions and research centers as well as consumer genomics, biotechnology, pharmaceutical, and agri-genomics companies.

RNA-Seq : Starting at $70.00 USD per sample
ChIP-Seq : Starting at $45.00 USD per sample

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Our Services (24)


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RNA-Seq Data Analysis

Starting at $70.00 per sample

Use our fast and super easy to use software and analyze your RNA-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.

The RNA-Seq analysis on Basepair includes:

QC of raw reads to calculate sequencing quality score, contamination, etc.
Alignment to reference genome (STAR or... Show more »

Use our fast and super easy to use software and analyze your RNA-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.

The RNA-Seq analysis on Basepair includes:

QC of raw reads to calculate sequencing quality score, contamination, etc.
Alignment to reference genome (STAR or Tophat2)
Post-aligment metrics
Files for visualization in IGV or UCSC genome browser
Digital expression count
Differential gene expression (DESeq2)
List of genes going up and down
Heatmap
Volcano plot

The following reference genomes are supported:
* human (hg38, hg19)
* mouse (mm10, mm9)
* zebrafish (danRer10, zv9)
* Arabidopsis thaliana (TAIR10)
* Saccharomyces cerevisiae (sacCer3)
* Solanum lycopersicum (Solgen 2.40)
* Streptococcus sanguinis SK36\
* Xenopus laevis (X. laevis v9.1)
* Xenopus tropicalis (xenTro7)
* Zebra finch (taeGut2)

We also support ERCC spike-in control analysis.

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Human Xenopus (frog) Mouse Saccharomyces cerevisiae Zebrafish C. elegans Tophat Cufflinks Private Cloud Servers DEseq Star RNA-Seq RNA Illumina Illumina TruSeq Show 15 more tags Show less

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ChIP-Seq Data Analysis

Chromatin immunoprecipitation-sequencing data analysis
Starting at $45.00 per sample

Use our fast and super easy to use software and analyze your ChIP-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.

The ChIP-Seq analysis on Basepair includes:

  • QC of raw reads to calculate sequencing quality score, contamination, etc.
  • Trim low quality bases
  • Alignment to... Show more »

Use our fast and super easy to use software and analyze your ChIP-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.

The ChIP-Seq analysis on Basepair includes:

  • QC of raw reads to calculate sequencing quality score, contamination, etc.
  • Trim low quality bases
  • Alignment to reference genome (Bowtie2)
  • Remove duplicate reads
  • Files for visualization in IGV or UCSC genome browser
  • Peaks
  • Annotation and genomic distribution of peaks
  • Motif analysis

The following reference genomes are supported:
* human (hg38, hg19)
* mouse (mm10, mm9)
* zebrafish (danRer10, zv9)
* Arabidopsis thaliana (TAIR10)
* Saccharomyces cerevisiae (sacCer3)
* Solanum lycopersicum (Solgen 2.40)
* Streptococcus sanguinis SK36\
* Xenopus laevis (X. laevis v9.1)
* Xenopus tropicalis (xenTro7)
* Zebra finch (taeGut2)

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Ion Torrent Human Xenopus (frog) Mouse Saccharomyces cerevisiae Zebrafish C. elegans Drosophila (Fruit Fly) Bowtie Private Cloud Servers Illumina Show 11 more tags Show less

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ATAC-Seq

Assay for Transposase-Accessible Chromatin with High Throughput Sequencing
Starting at $40.00 per sample

ATAC-Seq Data Analysis

Use our fast and super easy to use software and analyze your ATAC-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.
The ATAC-Seq analysis on Basepair includes:

QC of raw reads to calculate sequencing quality score, contamination, etc.
Files for... Show more »

ATAC-Seq Data Analysis

Use our fast and super easy to use software and analyze your ATAC-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.
The ATAC-Seq analysis on Basepair includes:

QC of raw reads to calculate sequencing quality score, contamination, etc.
Files for visualization in IGV or UCSC genome browser
ATAC-Seq Alignment (Bowtie 2)
ATAC-Seq Peak Calling (MACS2)
Heatmap
Volcano plot

The following reference genomes are supported:
* human (hg38, hg19)
* mouse (mm10, mm9)
* zebrafish (danRer10, zv9)
* Arabidopsis thaliana (TAIR10)
* Saccharomyces cerevisiae (sacCer3)
* Solanum lycopersicum (Solgen 2.40)
* Streptococcus sanguinis SK36\
* Xenopus laevis (X. laevis v9.1)
* Xenopus tropicalis (xenTro7)
* Zebra finch (taeGut2)

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Ion Torrent Human Xenopus (frog) Mouse Saccharomyces cerevisiae Zebrafish C. elegans Drosophila (Fruit Fly) Private Cloud Servers Genomics Illumina Show 11 more tags Show less

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NGS Data Analysis

Next generation sequencing data analysis
Price on request

Analyze your NGS data in hours. Upload your raw data, choose among several high quality workflows for RNA-Seq, ChIP-Seq, DNA-Seq, etc. and get results in an hour.

Analyze your NGS data in hours. Upload your raw data, choose among several high quality workflows for RNA-Seq, ChIP-Seq, DNA-Seq, etc. and get results in an hour.

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Human Mouse Saccharomyces cerevisiae Zebrafish C. elegans Drosophila (Fruit Fly) Tophat Cufflinks Bowtie Private Cloud Servers DEseq Star RNA DNA Illumina Show 15 more tags Show less

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DNA Sequencing Data Analysis

Starting at $40.00 per sample

DNA Sequencing Data Analysis

Use our fast and super easy to use software and analyze your DNA-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.
The DNA-Seq analysis on Basepair includes:

QC of raw reads to calculate sequencing quality score, contamination, etc.
Files for... Show more »

DNA Sequencing Data Analysis

Use our fast and super easy to use software and analyze your DNA-Seq data in 1-2 hours.

You just need the raw fastq files provided by your sequencing core.
The DNA-Seq analysis on Basepair includes:

QC of raw reads to calculate sequencing quality score, contamination, etc.
Files for visualization in IGV or UCSC genome browser
CRISPR - Ebert Lab
DNA-Seq QC, Alignment
Variant Calling (FreeBayes)
List of genes going up and down
Heatmap
Volcano plot

The following reference genomes are supported:
* human (hg38, hg19)
* mouse (mm10, mm9)
* zebrafish (danRer10, zv9)
* Arabidopsis thaliana (TAIR10)
* Saccharomyces cerevisiae (sacCer3)
* Solanum lycopersicum (Solgen 2.40)
* Streptococcus sanguinis SK36\
* Xenopus laevis (X. laevis v9.1)
* Xenopus tropicalis (xenTro7)
* Zebra finch (taeGut2)

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Ion Torrent Human Mouse Saccharomyces cerevisiae Zebrafish C. elegans Drosophila (Fruit Fly) Private Cloud Servers DNA Genomics Illumina Show 11 more tags Show less

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Nucleic Acid Services

Price on request
Request a quote for more information about this service.

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Sequencing Data Analysis and Management

Price on request
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Biomolecular Interaction Analysis

Price on request
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Protein-DNA Interaction Analysis

Price on request
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Nucleic Acid Data Analysis

Price on request
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Biology

Price on request
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DNA/RNA Analysis and Quality Control

Price on request
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Epigenetic Studies

Price on request
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Genomics Consulting

Price on request
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Whole Genome Assembly

Price on request
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DNA Services

Price on request

DNA Services

DNA Services

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Nucleic Acid Analysis

Price on request
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DNA Sequencing

Price on request

DNA Sequencing Services

DNA Sequencing Services

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Gene Set Enrichment Analysis

Price on request
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Project Management

Price on request
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miRNA-Sequencing Data Analysis

Price on request
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Biochemistry & Molecular Biology

Price on request
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Whole Exome Sequencing Data Analysis

Price on request
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Whole Genome Sequencing Data Analysis

Price on request
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  • Positive review for RNA-Seq Data Analysis:

    May 2017

    "Fast, excellent and reasonably priced...you CAN get all three!! Thank you to the folks at Basepair for helping us deal with some difficult RNA Seq data."

Basepair has not received any endorsements.