ArticleBMC bioinformatics2016
Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Synaptotagmin 11 scaffolds MKK7-JNK signaling process to promote stem-like molecular subtype gastric cancer oncogenesis.Journal of experimental & clinical cancer research : CR · 2022Article
- An Integrated Approach Reveals DNA Damage and Proteotoxic Stress as Main Effects of Proton Radiation inInternational journal of molecular sciences · 2022Article
- A genome-scale yeast library with inducible expression of individual genes.Molecular systems biology · 2021Article
- Gene Loss Predictably Drives Evolutionary Adaptation.Molecular biology and evolution · 2020Article
- Bioinformatics services for analyzing massive genomic datasets.Genomics & informatics · 2020Article
- Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments.Nature protocols · 2019Article
- bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPooled library screen analysis using shRNAs or CRISPR-Cas9 hold great promise to genome-wide functional studies. While pooled library screens are effective tools, erroneous barcodes can potentially be generated during the production of many barcodes. However, no current tools can distinguish erroneous barcodes from PCR or sequencing errors in a data preprocessing step.
resultsWe developed the Barcas program, a specialized program for the mapping and analysis of multiplexed barcode sequencing (barcode-seq) data. For fast and efficient mapping, Barcas uses a trie data structure based imperfect matching algorithm which generates precise mapping results containing mismatches, shifts, insertions and deletions (indel) in a flexible manner. Barcas provides three functions for quality control (QC) of a barcode library and distinguishes erroneous barcodes from PCR or sequencing errors. It also provides useful functions for data analysis and visualization.
conclusionsBarcas is an all-in-one package providing useful functions including mapping, data QC, library QC, statistical analysis and visualization in genome-wide pooled screens.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.