getBAM: Downloads an SRA accession from an experiment S3 directory 1)...
In serratus-bio/tantalus: R Data Exploration for Serratus
getBAM R Documentation
Downloads an SRA accession from an experiment S3 directory
1) download bam file
2) sort bam file (samtools)
3) index bam file (samtools)
Description
Implicit system dependcies
- samtools
- aws cli
Usage
getBAM(sra, s3_path = "s3://lovelywater2/", local_path = "bam")
Arguments
sra
SRA accession to download
s3_path
a string s3 path holding .summary files
local_path
local path into which to download the data [bam]
Examples
getBam(sra = 'SRR5447135', s3_path = 's3://lovelywater2/bam/')
serratus-bio/tantalus documentation built on March 29, 2023, 9:39 p.m.
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| getBAM | R Documentation |
Downloads an SRA accession from an experiment S3 directory 1) download bam file 2) sort bam file (samtools) 3) index bam file (samtools)
Description
Implicit system dependcies - samtools - aws cli
Usage
getBAM(sra, s3_path = "s3://lovelywater2/", local_path = "bam")
Arguments
sra |
SRA accession to download |
s3_path |
a string s3 path holding .summary files |
local_path |
local path into which to download the data [bam] |
Examples
getBam(sra = 'SRR5447135', s3_path = 's3://lovelywater2/bam/')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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