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searching for SAMtools 11 found (28 total)

alternate case: sAMtools

BioRuby (503 words) [view diff] case mismatch in snippet view article find links to article

poi 0.13.3 4 Bio gem Software generator for Ruby 1.36 5 Bio samtools Binder of samtools for Ruby 2.1.0 6 t2 server Support for interacting with the taverna

UGENE (1,486 words) [view diff] exact match in snippet view article find links to article

sequencing data (BAM files) using UGENE Assembly Browser Variant calling with SAMtools RNA-Seq data analysis with Tuxedo pipeline (TopHat, Cufflinks, etc.) ChIP-seq

BED (file format) (1,480 words) [view diff] case mismatch in snippet view article

Retrieved 2 October 2019. "The Browser Extensible Data (BED) format" (PDF). samtools.github.io. "GA4GH BED v1.0: A formal standard sets ground rules for genomic

Tabix (113 words) [view diff] case mismatch in snippet view article find links to article

Browser. University of California, Santa Cruz. Retrieved January 26, 2021. "Samtools/Htslib". GitHub. 2 May 2022. File format specification Command-line utility

Gonçalo Abecasis (1,042 words) [view diff] exact match in snippet view article find links to article

Data Processing Subgroup (2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352

RNA-Seq (11,031 words) [view diff] exact match in snippet view article find links to article

similar to DNA variant calling and often employs the same tools (including SAMtools mpileup and GATK HaplotypeCaller) with adjustments to account for splicing

SNV calling from NGS data (3,217 words) [view diff] exact match in snippet view article find links to article

JointSNVMix MaCH Magnolia DCNN NeuSomatic NGSEP Pisces Platypus realSFS Reveel SAMtools SNVmix SOAPsnp SomaticSeq SomaticSniper Strelka VarDict VarScan Nielsen

List of filename extensions (M–R) (1,430 words) [view diff] exact match in snippet view article

Processing Subgroup (2009) (2009). "The Sequence alignment/map (SAM) format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352

Transcriptomics technologies (12,516 words) [view diff] exact match in snippet view article find links to article

Abecasis G, Durbin R (August 2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–9. doi:10.1093/bioinformatics/btp352. PMC 2723002

ANNOVAR (3,454 words) [view diff] case mismatch in snippet view article find links to article

accepted by the convert2annovar.pl include the following: Variant Call Format Samtools genotype-calling pileup format Illumina export format from GenomeStudio

List of RNA-Seq bioinformatics tools (20,371 words) [view diff] exact match in snippet view article find links to article

RNA-Seq. The pipeline employs tools like Bowtie, TopHat, ArrayExpressHTS and SAMtools. Also, edgeR or DESeq to perform differential expression. MultiDE Myrna