Description Usage Arguments Examples
The NGS read alignment using hisat2 for multiple samples. The input and output directory must be created by 'rskoseq::project_rnsq'.
1 | rep_hisat2(alndir, idx, project, fqdir, paired, suffix_fq, ...)
|
alndir |
character: the name of alignment directory. results output |
idx |
character: the fully path of hisat2 index name. |
project |
logical:default is TRUE. If does not create project directory using rskoseq::project_rnsq, it is FALSE |
fqdir |
character: the fully path of fastq files. The default is 'paste0(dirname(alndir), "/fastq")'. If this directory containing still analyzed fastq and additional fastq files, |
paired |
logical: paired or single read. If paired end, the names of fastq file must be "_R1" and "_R2". |
suffix_fq |
character: suffix of fastq files. The default is ".fastq.gz" |
... |
additional hisat2 options. E.g. "–no-spliced-alignment –rna-strandness R" |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## Not run:
# project TRUE (all result created at directories predetermined by 'project_rnsq')
alnd <- "~/pub/sampledata/rnaseq/project1/test1.h2"
idx <- "~/db/index/hisat2_idx/CriGri_1.0.ens.add"
unlink(alnd, recursive = T)
rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "test1.h2", "hisat2")
rskoseq::rep_hisat2(alndir = alnd, idx = idx, paired = F)
system(paste("tree", alnd))
# paired
alnd <- "~/pub/sampledata/rnaseq/project1/test2.h2"
fqd <- "~/pub/sampledata/rnaseq/project1/paired_fastq"
unlink(alnd, recursive = T)
rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "test2.h2", "hisat2")
adopt <- "--rna-strandness RF --no-softclip --dta"
rskoseq::rep_hisat2(alndir = alnd, idx = idx, fqdir = fqd, suffix_fq = "_sub.fastq.gz",
paired = T, ... = adopt)
# project FALSE (all result create under the alignment directory)
alnd <- "~/pub/sampledata/rnaseq/project1"
fqd <- "~/pub/sampledata/rnaseq/project1/fastq"
rep_hisat2(alndir = alnd, project = F, idx = idx, fqdir = fqd, paired = FALSE)
## End(Not run)
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