Run multiple kallisto instances. It includes an index with all protein coding genes and retrocopies
157
$ docker run
--rm
-u $(id -u):$(id -g) -v $(pwd):$(pwd)
-w $(pwd)
kallisto kallisto_pipeline -p "prefix" -t 10 -j 10 [-i "index"] FILES
USAGE kallisto_pipeline
OPTIONS: -p prefix -t number of threads for samtools and kallisto -j max number of jobs to run in parallel -i path to kallisto index file. Default to "gencode.v19.all_pc_w_rtc.idx" at root /
ARGUMENTS: A list of bam and tar.gz files. Fastq files are extracted from bam using "samtools fastq". If the file is a tarball, then it is assumed that the fastq files are archived inside this tarball.
Content type
Image
Digest
Size
1.4 GB
Last updated
over 8 years ago
docker pull thiagomiller/kallisto