blatListedSet

DNAStringSet object containing sequences to be aligned against the reference.

dnaSetList

parameters to be passed to <code><a href="/link/blatSeqs?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::blatSeqs">blatSeqs</a></code>.

Align sequences from a listed DNAStringSet object returned from
<code><a href="/link/extractSeqs?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::extractSeqs">extractSeqs</a></code> to an indexed reference genome using
gfServer/gfClient protocol or using standalone BLAT and return the psl file
as a GRanges object. This function heavily relies on defaults of
<code><a href="/link/blatSeqs?package=hiReadsProcessor&version=1.8.2" rd-options="" data-mini-rdoc="hiReadsProcessor::blatSeqs">blatSeqs</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

blatListedSet function

parameters to be passed to <code><a href="blatSeqs" rd-options="">blatSeqs</a></code>.

Align sequences from a listed DNAStringSet object returned from
<code><a href="extractSeqs" rd-options="">extractSeqs</a></code> to an indexed reference genome using
gfServer/gfClient protocol or using standalone BLAT and return the psl file
as a GRanges object. This function heavily relies on defaults of
<code><a href="blatSeqs" rd-options="">blatSeqs</a></code>.

blatListedSet: Align a listed DNAStringSet to a reference using gfClient or standalone BLAT.

Description

Usage

Arguments

Value

See Also