run_kallisto: 'Run kallisto quant.'

In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description

kallisto quant

Usage

run_kallisto(df, single = TRUE, l = 200, s = 20,
  idx = "~/dbcenter/AGP/AGPv2/ZmB73_5a_WGS_exons.kallisto.idx",
  email = NULL, jobid = "run_kquant", runinfo = c(TRUE, "jclarke",
  "1", "8G", "8:00:00"))

Arguments

df	Input files, [data.frame, col: outdir, fq (SE) or fq1 and fq2 (PE)]
single	Single (or PE) end fastq [TRUE(FALSE)].
l	Estimated average fragment length [number, default=200].
s	Estimated standard deviation of fragment length [number, default=20].
idx	Full path of Kallisto Index file, [chr, "/lustre/work/jyanglab/jyang21/dbcenter/AGP/AGPv4/Zea_mays.AGPv4.cdna.all.kallisto.idx"]
run	Parameters control the array job partition. A vector of c(TRUE, "bigmemh", "1", "8:00:00"): 1) run or not, 2) -p partition name, 3) –ntasks and 4) –times.

Details

see more detail about fastq-dump with Aspera downloading: https://pachterlab.github.io/kallisto/manual

Value

return a batch of shell scripts to run.

Examples

### build kallisto idex
 kallisto index -i ZmB73_5a_WGS_exons.kallisto.idx ZmB73_5a_WGS_exons.fasta.gz
 kallisto quant -i ~/dbcenter/AGP/AGPv2/ZmB73_5a_WGS_exons.kallisto.idx --plaintext -o .
--single -l 200 -s 20 SRR957415.sra.fastq SRR957416.sra.fastq > test.txt

yangjl/huskeR documentation built on Sept. 2, 2021, 5:38 a.m.