BamTools: a C++ API and toolkit for analyzing and managing BAM files

Barnett, Derek W.; Garrison, Erik; Quinlan, Aaron R.; Strömberg, Michael; Marth, Gábor

doi:10.1093/bioinformatics/btr174

Cited by 892 publications

(701 citation statements)

References 7 publications

Supporting

Mentioning

701

Contrasting

Order By: Relevance

“…Indel detection was disabled, and only unique alignments were reported using the -g option; all other options were set to default. BAMTools (v 1.0.2) (Barnett et al, 2011) was used to calculate mapping result statistics. The BAM file for each sample was sorted by leftmost coordinates using the SAMTools sort function (v 0.1.12a) (Li et al, 2009).…”

Section: Identification Of Snps In Rna-seq Datamentioning

confidence: 99%

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

et al. 2017

View full text Add to dashboard Cite

Tocopherols, tocotrienols, and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot Arabidopsis thaliana, which has green, photosynthetic seeds, but our understanding of tocochromanol accumulation in major crops, whose seeds are nonphotosynthetic, remains limited. To understand the genetic control of tocochromanols in grain, we conducted a joint linkage and genome-wide association study in the 5000-line U.S. maize (Zea mays) nested association mapping panel. Fifty-two quantitative trait loci for individual and total tocochromanols were identified, and of the 14 resolved to individual genes, six encode novel activities affecting tocochromanols in plants. These include two chlorophyll biosynthetic enzymes that explain the majority of tocopherol variation, which was not predicted given that, like most major cereal crops, maize grain is nonphotosynthetic. This comprehensive assessment of natural variation in vitamin E levels in maize establishes the foundation for improving tocochromanol and vitamin E content in seeds of maize and other major cereal crops.

show abstract

Section: Identification Of Snps In Rna-seq Datamentioning

confidence: 99%

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Reads that were mapped to multiple positions were filtered out by Bamtools (Barnett et al, 2011). The Cuffdiff software (2.1.0) (Trapnell et al, 2010) was used to quantify the raw read count in each gene, using the version 5a gene annotation (working set genes) provided by the maize genome sequencing project .…”

Section: Bioinformaticsmentioning

confidence: 99%

Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation

et al. 2014

View full text Add to dashboard Cite

Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize (Zea mays) leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialized ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally derived fringe. Recessive liguleless1 mutants lack ligules and auricles and have upright leaves. We used laser microdissection and RNA sequencing to identify genes that are differentially expressed in discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation and compared transcript accumulation in wild-type and liguleless1-R mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these "ligule genes" have also been shown to function during leaf initiation or lateral branching and intersect multiple hormonal signaling pathways. We propose that genetic modules utilized in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.

show abstract

“…For RNA-seq, reads were mapped onto the hg19 genome and exon-exon junctions by splice-aware aligner Tophat [47], using the known gene model annotation from Ensembl release 62. Reads with an unmapped mate or multi-mapped location were filtered out using Bamtools [48] and PCR or sequencing optical duplicates were marked and removed by Picard [49]. Using NCBI dbSNP build 132, multiple sequence local realignment around InDels and base quality recalibration was performed by GATK (The Genome Analysis Toolkit) [50] to correct likely misalignments.…”

Section: Sequence Data Mapping and Processingmentioning

confidence: 99%

Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer

Wyatt

Wang

et al. 2014

Genome Biol

View full text Add to dashboard Cite

Background: Genomic analyses of hundreds of prostate tumors have defined a diverse landscape of mutations and genome rearrangements, but the transcriptomic effect of this complexity is less well understood, particularly at the individual tumor level. We selected a cohort of 25 high-risk prostate tumors, representing the lethal phenotype, and applied deep RNA-sequencing and matched whole genome sequencing, followed by detailed molecular characterization.

show abstract

BamTools: a C++ API and toolkit for analyzing and managing BAM files

Abstract: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

Cited by 892 publications

References 7 publications

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation

Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer

Contact Info

Product

Resources

About