map: map takes cDNA reads (fastQ format) and maps them onto...

In etheleon/metamaps: MetamapsDB: R package for querying Metagenomics data against Metabolic Pathways and Gene Centric Assemblies

Description

uses blat to map the mRNA to the contigs fasta and returns the tabular blast format blat was chosen for its ability to show multiple hits https://www.biostars.org/p/17613/

Usage

map(reads, contigs)

Arguments

reads	Shortread object or path to short reads file in fastq format
contigs	path to contig file in fa format

Examples

## Not run: 
# newbler2/K00927
#    454AllContigs.fna
#    input
#        K00927.1.fq
#        K00927.2.fq

lapply(kois, function(ko){
    read1 = sprintf("./newbler2/%s/input/%s.2.fq", ko, ko)
    if file.exists(read1)
        read1.fq = read1 %>% readFastq
    read2 = sprintf("./newbler2/%s/input/%s.2.fq", ko, ko)
    if file.exists(read2)
        read2.fq = read2 %>% readFastq
    combined = c(grep.cDNA(read1.fq),grep.cDNA(read2.fq))
    contigs = sprintf("./newbler2/%s/454AllContigs.fna", ko)
    output = sprintf("./blat/%s.m8", ko)
    blast8 = map(combined, contigs, output) %<>% tbl_df
})

## End(Not run)

etheleon/metamaps documentation built on May 16, 2019, 9:05 a.m.