Fast gapped-read alignment with Bowtie 2

Langmead, Ben; Salzberg, Steven L.

doi:10.1038/nmeth.1923

Cited by 45,711 publications

(35,930 citation statements)

References 13 publications

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“…Briefly, RNA-seq reads were first trimmed using Trimmomatic 38 . Trimmed reads were aligned to the RefSeq hg38 genome and transcriptome (GRCh38.2) using Bowtie2 (Ref 39 ) and TopHat 40 , respectively. The resulting transcriptome alignments were processed by RSEM to estimate the abundance of RefSeq transcripts, in Transcripts Per kilobase Million (TPM).…”

Section: Methodsmentioning

confidence: 99%

Global delay in nascent strand DNA methylation

Charlton

Downing

Smith

et al. 2018

Nat Struct Mol Biol

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Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitotically propagated over many generations with extraordinarily high fidelity. Here, we combine BrdU labeling and immunoprecipitation with genome-wide bisulfite sequencing to explore the inheritance of cytosine methylation onto newly replicated DNA in human cells. Globally, we observe a pronounced lag between the copying of genetic and epigenetic information that is reconsolidated within hours to accomplish faithful mitotic transmission. Populations of arrested cells show a global reduction of lag induced intermediate CpG methylation when compared to proliferating cells, while sites of transcription factor engagement appear cell-cycle invariant. Alternatively, the cancer cell line HCT116 preserves global epigenetic heterogeneity independently of cell-cycle arrest. Taken together, our data suggest that heterogeneous methylation largely reflects asynchronous proliferation, but is intrinsic to actively engaged cis-regulatory elements and cancer.

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Section: Methodsmentioning

confidence: 99%

Global delay in nascent strand DNA methylation

Charlton

Downing

Smith

et al. 2018

Nat Struct Mol Biol

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“…Each barcode‐specific set of ORF reads can then be analyzed with respect to mutations. Bowtie2 software (Langmead & Salzberg, 2012) is used to align reads to the ORF template, PCR duplicates are removed, and nucleotide variants called using samtools pileup (Li et al , 2009). Given limited read lengths, identification of longer indels is not straightforward.…”

Section: Methodsmentioning

confidence: 99%

“…For DMS‐TileSeq, raw sequencing reads were aligned to the reference ORF cDNA sequences using Bowtie‐2 (Langmead & Salzberg, 2012) and a custom Perl script was used to parse and compare the forward and reverse read alignment files to count the number of co‐occurrences of a codon change in both paired reads. Mutational counts in each condition were normalized to sequencing depth at the respective position.…”

Section: Methodsmentioning

confidence: 99%

A framework for exhaustively mapping functional missense variants

Weile

Sun

Coté

et al. 2017

Molecular Systems Biology

172

286

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Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin‐like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.

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“…Mapping was carried out against the reference genome obtained from the Candida Genome Database [19]. We used the splice junction sensitive mapper Tophat 2.01.13 [32] with default settings, and mapped by applying the bowtie 2.2.4 [33] short read mapper. The counts per gene were estimated by using flux-capacitor [34].…”

Section: Methodsmentioning

confidence: 99%

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis

et al. 2018

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Lipid mediators, derived from arachidonic acid metabolism, play an important role in immune regulation. The functions of bioactive eicosanoids range from modulating cytokine signaling and inflammasome formation to anti-inflammatory and pro-resolving activities. Human pathogenic fungi such as Candida albicans, Candida parapsilosis, Cryptococcus neoformans and Aspergillus fumigatus have been shown to produce such lipid mediators, associated with their virulence. To date, investigations into the molecular mechanisms of fungal eicosanoid biosynthesis in different species have revealed that several genes are associated with prostaglandin production. However, these routes remain uncharacterized in C. parapsilosis with early results suggesting it uses pathways distinct from those found in C. albicans. Therefore, we aimed to identify and characterize C. parapsilosis genes involved in eicosanoid biosynthesis. Following arachidonic acid treatment of C. parapsilosis cells, we identified several genes interfering with prostaglandin production. Out of the identified genes, homologues of a multi copper oxidase (FET3), an Acyl-CoA thiolase (POT1) and an Acyl-CoA oxidase (POX1-3) were found to play a significant role in prostaglandin synthesis. Furthermore, all three genes were confirmed to enhance C. parapsilosis pathogenicity, as the corresponding deletion mutants were cleared more efficiently by human macrophages and induced higher levels of pro-inflammatory cytokines. In addition, the mutants were less virulent than the wild-type strain in a mouse model of systemic infection. Taken together, we identified three genes that regulate eicosanoid biosynthesis in C. parapsilosis and impact the fungus’ virulence.

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Fast gapped-read alignment with Bowtie 2

Cited by 45,711 publications

References 13 publications

Global delay in nascent strand DNA methylation

Global delay in nascent strand DNA methylation

A framework for exhaustively mapping functional missense variants

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis

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