bowtie2Index.Rd
This function executes the docker container bowtie2 where bowtie2-2.2.9 is installed. The index is created using ENSEMBL genome fasta file. User needs to provide the URL for ENSEMBL genome located in the ENSEMBL ftp
bowtie2Index( group = c("sudo", "docker"), genome.folder = getwd(), ensembl.urlgenome = NULL, ensembl.urlgtf = NULL, threads = 1 )
group, | a character string. Two options: |
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genome.folder, | a character string indicating the folder where the indexed reference genome for Bowtie will be located |
ensembl.urlgenome, | a character string indicating the URL from ENSEMBL ftp for the unmasked genome sequence of interest |
ensembl.urlgtf, | a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest |
threads, | a number indicating the number of cores to be used from the application |
The indexed Bowtie genome reference sequence
if (FALSE) { #running rsemstar index for human bowtie2Index(group="docker",genome.folder="/data/scratch/hg38bowtie2", ensembl.urlgenome= "ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz", ensembl.urlgtf= "ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz", threads=8) }