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Data Import

Import Next-Generation Sequencing (NGS) data and feature annotations from SAM, BAM, FASTA, FASTQ, GTF, and GFF files

Import NGS data stored in different file formats such as FASTA, FASTQ, SAM, and BAM files. Read feature annotations from GTF and GFF files. Use various objects to access and manage NGS data. For instance, the BioIndexedFile object lets you efficiently access text files with nonuniform-size entries, such as sequences and annotations. Use the object to access individual entries or a subset of entries when the source file is too big to fit in memory. Use the BioMap and BioRead objects to store and manage sequence read data containing information on headers, qualities, and alignments.


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fastainfoReturn information about FASTA file
fastareadRead data from FASTA file
fastawriteWrite to file using FASTA format
fastqinfoReturn information about FASTQ file
fastqreadRead data from FASTQ file
fastqwriteWrite to file using FASTQ format
saminfoReturn information about SAM file
samsortSort SAM files
samreadRead data from SAM file
baminfoReturn information about BAM file
bamreadRead data from BAM file
bamsortSort BAM files
getDataCreate structure containing subset of data from GTFAnnotation or GFFAnnotation object
getExonsReturn table of exons from GTFAnnotation object
getFeatureNamesRetrieve unique feature names from GTFAnnotation or GFFAnnotation object
getGeneNamesRetrieve unique gene names from GTFAnnotation object
getGenesReturn table of unique genes in GTFAnnotation object
getIndexReturn index array of annotations from GTFAnnotation or GFFAnnotation object
getRangeRetrieve range of annotations from GTFAnnotation or GFFAnnotation object
getReferenceNamesRetrieve reference names from GTFAnnotation or GFFAnnotation object
getSegmentsReturn table of non-overlapping segments from GTFAnnotation object
getSubsetRetrieve subset of elements from GTFAnnotation or GFFAnnotation object
getTranscriptNamesRetrieve unique transcript names from GTFAnnotation object
getTranscriptsReturn table of unique transcripts in GTFAnnotation object
cuffgffreadFilter and convert GFF and GTF files
cuffgtf2samConvert GTF files to SAM files


BioReadContain sequence reads and their quality data
BioMapContain sequence, quality, alignment, and mapping data
BioIndexedFileAllow quick and efficient access to large text file with nonuniform-size entries
GFFAnnotationContain General Feature Format (GFF) annotations
GTFAnnotationContain Gene Transfer Format (GTF) annotations