Hello, I'm new to this package and field of study. I've been following the ATACseqQC Quick Start guide to process genomic data, and I realized in section 2.4.1 (http://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html#adjust-the-read-start-sites) they assign "seqlev" to be "chr1":
## files will be output into outPath outPath <- "splited" dir.create(outPath) ## shift the coordinates of 5'ends of alignments in the bam file library(BSgenome.Hsapiens.UCSC.hg19) seqlev <- "chr1" ## subsample data for quick run <--------- here's the assignment which <- as(seqinfo(Hsapiens)[seqlev], "GRanges") gal <- readBamFile(bamfile, tag=tags, which=which, asMates=TRUE, bigFile=TRUE) shiftedBamfile <- file.path(outPath, "shifted.bam") gal1 <- shiftGAlignmentsList(gal, outbam=shiftedBamfile)
Can someone please explain what it means to subsample here and how the assignment right under it for "which" would change if I wanted to avoid subsampling? Thank you!