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Into destination], using filter] as the filter The original file is then separately filtered Instances, in which case destination must be a character vector Time-efficient to filter using bamWhich, bamFlag, andīamSimpleCigar, if appropriate, than to supplyįilterRules. An index file is created on theĭestination when indexDestination=TRUE. Return values are used to include (when TRUE)Ĭorresponding records in the filtered BAM file. Logical vector equal to the number of rows of theĭataFrame. Instance should expect a single DataFrame argument representingĪll information specified by param. These records are then parsed toĪ DataFrame and made available for further filtering by Param are accumulated to a default of yieldSize =ġ000000 records (change this by specifying yieldSize whenīamFile-class). Records satisfying theīamWhich bamFlag and bamSimpleCigar criteria of The 'BAM' file is sortedĪnd an index created on the destination (with extension '.bai') whenĪsSam converts 'BAM' files to 'SAM' files, equivalent toįilterBam parses records in file. ForĪsBam asSam, and sortBam this is without theĪ GRanges() instance with destination. The sorted, filtered, or merged output file will be created. The character(1) file name of the location where
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The character(1) name of the index file of the 'BAM' fileīeing processed this is given without the '.bai' extension. For mergeBam, must satisfy length(files) >= The character() file names of the ‘BAM’ file to be The character(1) file name of the ‘BAM’ ('SAM' for , region = GRanges (), overwrite = FALSE, header = character (), byQname = FALSE, addRG = FALSE, compressLevel1 = FALSE, indexDestination = FALSE ) ) # S4 method for signature 'character' mergeBam ( files, destination. ) # S4 method for signature 'character' indexBam ( files. , byQname = FALSE, maxMemory = 512 ) indexBam ( files. ) # S4 method for signature 'character' sortBam ( file, destination. , filter = FilterRules (), indexDestination = TRUE, param = ScanBamParam ( what = scanBamWhat ())) sortBam ( file, destination. ) # S4 method for signature 'character' filterBam ( file, destination, index = file. , overwrite = FALSE ) filterBam ( file, destination, index = file. ) # S4 method for signature 'character' asSam ( file, destination = sub ( "\\.bam", "", file ). , overwrite = FALSE, indexDestination = TRUE ) asSam ( file, destination = sub ( "\\.bam", "", file ). ) # S4 method for signature 'character' asBam ( file, destination = sub ( "\\.sam(\\.gz)?", "", file ). ) # S4 method for signature 'character' scanBamHeader ( files. , param = ScanBamParam ()) idxstatsBam ( file, index = file. , param = ScanBamParam ( what = scanBamWhat ())) countBam ( file, index = file.
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scanBam: Import, count, index, filter, sort, and merge 'BAM' (binary.Rsamtools-package: 'samtools' aligned sequence utilities interface.RsamtoolsFileList-class: A base class for managing lists of Rsamtools file references.RsamtoolsFile-class: A base class for managing file references in Rsamtools.readPileup: Import samtools 'pileup' files.quickBamFlagSummary: Group the records of a BAM file based on their flag bits and.PileupFiles-class: Represent BAM files for pileup summaries.pileup: Use filters and output formats to calculate pile-up.indexTabix: Compress and index tabix-compatible files.headerTabix: Retrieve sequence names defined in a tabix file.FaFile-class: Manipulate indexed fasta files.defunct: Rsamtools Deprecated and Defunct.BamViews-class: Views into a set of BAM files.BamFile-class: Maintain and use BAM files.ApplyPileupsParam-class: Parameters for creating pileups from BAM files.applyPileups: Apply a user-provided function to calculate pile-up.