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Arpi Beshlikyan
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@arpi-beshlikyan-23945
Last seen 3.8 years ago
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!
seqlev is used to tell readBamFile only read the "chr1" reads. If you do not want this, just set seqlev by all the seqnames in your bam file.
Thank you! I also realized that the "which" parameter is optional and I can just take it out.
Thank you! I also realized that the "which" parameter is optional and I can just take it out.
seqlev is used to tell readBamFile only read the "chr1" reads. If you do not want this, just set seqlev by all the seqnames in your bam file.