pairUpAlignments

a GRanges object with qNames ending in "atpersand pairname atpersand".

psl.rd

maximum gap allowed between end of pair1 and start of
pair2. Default is 2500 bp.

maxGapLength

should pairs be aligned to the same strand or in same
orientationin the reference genome? Default is TRUE. This is 'TRUE' because
pair2 reads are reverseComplemented when reading in data in
<code><a href="/link/findBarcodes?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::findBarcodes">findBarcodes</a></code>

sameStrand

use parallel backend to perform calculation with
<code><a href="/link/BiocParallel?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::BiocParallel">BiocParallel</a></code>. Defaults to TRUE. If no parallel backend is
registered, then a serial version is ran using <code><a href="/link/SerialParam?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::SerialParam">SerialParam</a></code>.

parallel

Given a GRanges object, the function uses specified gaplength parameter to
pair up reads where the qName column ends with "atpersand pairname atpersand"
which is outputted by <code><a href="/link/extractSeqs?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::extractSeqs">extractSeqs</a></code>.

hiReadsProcessor contains set of functions which allow
        users to process LM-PCR products sequenced using any platform.
        Given an excel/txt file containing parameters for
        demultiplexing and sample metadata, the functions automate
        trimming of adaptors and identification of the genomic product.
        Genomic products are further processed for QC and abundance
        quantification.

Nirav V Malani

hiReadsProcessor

Functions to process LM-PCR reads from 454/Illumina data

pairUpAlignments function

should pairs be aligned to the same strand or in same
orientationin the reference genome? Default is TRUE. This is 'TRUE' because
pair2 reads are reverseComplemented when reading in data in
<code><a href="findBarcodes" rd-options="">findBarcodes</a></code>

use parallel backend to perform calculation with
<code><a href="BiocParallel" rd-options="">BiocParallel</a></code>. Defaults to TRUE. If no parallel backend is
registered, then a serial version is ran using <code><a href="SerialParam" rd-options="">SerialParam</a></code>.

Given a GRanges object, the function uses specified gaplength parameter to
pair up reads where the qName column ends with "atpersand pairname atpersand"
which is outputted by <code><a href="extractSeqs" rd-options="">extractSeqs</a></code>.

pairUpAlignments: Pair up alignments in a GRanges object

Description

Usage

Arguments

Value

See Also

Examples