HISAT: a fast spliced aligner with low memory requirements

Kim, Daehwan; Langmead, Ben; Salzberg, Steven L.

doi:10.1038/nmeth.3317

Cited by 16,234 publications

(11,969 citation statements)

References 16 publications

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“…Reads were trimmed to the end if the mean Phred of a four nucleotide sliding window was less than 30 and only reads satisfying the minimum length of 20 nucleotides were allowed to survive. Reads surviving as a pair were aligned to reference genomes in a paired-end fashion using HISAT2 v2.1.0 [85], suppressing alignments resulting in fragments longer than 1000 nucleotides. Orphan R1 and R2 sequences from paired-end libraries and those coming from single-end runs were aligned using the single-end mode.…”

Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

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Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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“…For identification of exogenic transcripts, we aligned reads on the mm9 genome using HISAT2 60 with the option to authorize splicing events. From these alignments, we count the number of reads in sliding windows of 1kb (with a step of 600nt) taking each strand of the genome as separate.…”

Section: On-line Methodsmentioning

confidence: 99%

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer

Abdennur

Goloborodko

et al. 2017

Nature

993

114

1,115

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Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-large active and inactive compartments, and partitioning into sub-megabase domains (TADs). Yet, it remains unclear how these layers of organization form, interact with one another and impact genome functions. Here, we show that deletion of the cohesin-loading factor Nipbl, in mouse liver, leads to a dramatic reorganization of chromosomal folding. TADs and associated peaks vanish globally, even in the absence of transcriptional changes. In contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the 3D organization of the genome results from the interplay of two independent mechanisms: 1) cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; 2) cohesin-dependent formation of TADs, possibly by loop extrusion, which contributes to guide distant enhancers to their target genes.

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“…Libraries were made using the protocol of Zhong et al (2011) and sequenced using the Illumina NextSeq 500 to obtain single-end 75 bp reads. Reads were aligned to the 12X.2 version of the grapevine reference genome PN40024 using HISAT2 (Kim et al 2015) and the transcriptome was assembled using StringTie with the CRIBI functional annotation (Vitulo et al 2014). Transcribed genes were analyzed by fitting a linear model y = Xb + using Ballgown (Frazee et al 2015) where y was a vector holding the log 2 (FPKM + 1) values of genes with FPKM (Fragments Per Kilobase of transcript per Million reads sequenced) variances greater than one for each genotype; X was a design matrix that contained the indicator variables for the intercept and the genotypephase grouping; b was a vector holding the mean and the effect of the group value; and ∼ N(0, I 2 ) was a vector holding the error.…”

Section: Rna-seq Experimental Design and Analysismentioning

confidence: 99%

Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth

Prashar

Hornyik

Young³

et al. 2014

Theor Appl Genet

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Key message Downy mildew resistance across days post-inoculation, experiments, and years in two interspecific grapevine F 1 families was investigated using linear mixed models and Bayesian networks, and five new QTL were identified. Abstract Breeding grapevines for downy mildew disease resistance has traditionally relied on qualitative gene resistance, which can be overcome by pathogen evolution. Analyzing two interspecific F 1 families, both having ancestry derived from Vitis vinifera and wild North American Vitis species, across 2 years and multiple experiments, we found multiple loci associated with downy mildew sporulation and hypersensitive response in both families using a single phenotype model. The loci explained between 7 and 17% of the variance for either phenotype, suggesting a complex genetic architecture for these traits in the two families studied. For two loci, we used RNA-Seq to detect differentially transcribed genes and found that the candidate genes at these loci were likely not NBS-LRR genes. Additionally, using a multiple phenotype Bayesian network analysis, we found effects between the leaf trichome density, hypersensitive response, and sporulation phenotypes. Moderate-high heritabilities were found for all three phenotypes, suggesting that selection for downy mildew resistance is an achievable goal by breeding for either physical-or non-physical-based resistance mechanisms, with the combination of the two possibly providing durable resistance.

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HISAT: a fast spliced aligner with low memory requirements

Cited by 16,234 publications

References 16 publications

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Two independent modes of chromatin organization revealed by cohesin removal

Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth

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