Subsampling when adjusting the read start sites in the ATACseqQC guide
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@arpi-beshlikyan-23945
Last seen 3 months 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!

atacseqqc r • 152 views
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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.

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Thank you! I also realized that the "which" parameter is optional and I can just take it out.

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Entering edit mode

Thank you! I also realized that the "which" parameter is optional and I can just take it out.

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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.

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