Transcript Assembly
Easily perform transcript quantification using an input fastq file.
Overview
Takes in raw transcriptome data from an RNAseq experiment in and automatically assembles and quantifies transcripts. No reference genome required!
Run Transcript Assembly on Neurosnap
The Transcript Assembly online webserver allows anybody with a Neurosnap account to run and access Transcript Assembly, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Automatically assembles raw reads into valid transcripts without requiring a reference genome.
- Automatically quantifies transcripts.
- Automatically removes adapters and other unnecessary sequences.
- Automatically performs quality control on read data.
- Supports compressed fastq files.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access Transcript Assembly using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using Transcript Assembly in publications or research outputs.
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Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. PMID: 21572440; PMCID: PMC3571712. |
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Patro, R., Duggal, G., Love, M. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417–419 (2017). https://doi.org/10.1038/nmeth.4197 |
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Bushnell B. 2014. BBMap: a fast, accurate, splice-aware aligner [Internet]. Walnut Creek (CA): Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute; [cited 2025 Apr 8]. Available from: https://www.osti.gov/servlets/purl/1241166 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |