Description Usage Arguments Details Value Examples
kallisto quant
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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. |
see more detail about fastq-dump with Aspera downloading: https://pachterlab.github.io/kallisto/manual
return a batch of shell scripts to run.
1 2 3 4 | ### 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
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