Der All I am new with ATAC-Seq data and I have some QC questions We ran our first ATACseqQC experiments on MiSeq and got results that I would like to perform QC on… I cleaned up and mapped the fastq to the hg19 and was able to run most of your code for each sample, following this nice step by step approach: https://www.bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html#transcription-start-site-tss-enrichment-score
I am trying to get several ‘standard’ scores and results I got from one sample using the nice R package ATACseqQC See my questions below…
1 TSS Score
My results seem off with inf…. (according to what I understood, it should be >6 to be acceptable) Min. 0 1st Qu. 4.54695122 Median Inf Mean Inf 3rd Qu. Inf Max. Inf NA 24655
I did the following for the entire genome
gal <- readBamFile(bamfile, tag=character(0),asMates=TRUE, bigFile=TRUE) shiftedBamfile <- file.path(outPath, "shifted.bam") gal1 <- shiftGAlignmentsList(gal, outbam=shiftedBamfile) tsse <- TSSEscore(gal1, txs)
and I also tried with the tag identification for one chromosome
possibleTag <- combn(LETTERS, 2) possibleTag <- c(paste0(possibleTag[1, ], possibleTag[2, ]), paste0(possibleTag[2, ], possibleTag[1, ])) bamTop100 <- scanBam(BamFile(bamfile, yieldSize = 100), param = ScanBamParam(tag=possibleTag))[]$tag tags <- names(bamTop100)[lengths(bamTop100)==100] tags seqlev <- "chr1" which <- as(seqinfo(Hsapiens)[seqlev], "GRanges") gal <- readBamFile(bamfile, tag=tags, which=which, asMates=TRUE, bigFile=TRUE) shiftedBamfile <- file.path(outPath, "shifted.bam") gal1 <- shiftGAlignmentsList(gal, outbam=shiftedBamfile)
2 NFR Score:
I tried to compile an overall NFR score (all chrom) by computing the mean(nfr2$NFR_score) -0.54 [-0.58--0.49]
I am probably missing something as I don’t think this score can be negative? Should it be performed chrom by chrom?
3 The fraction of reads in called peak regions FRIP Score
It is the ratio nucleosome free/total obtained from libsize? NucleosomeFree.bam 601935 mononucleosome.bam 50970 dinucleosome.bam 33860 trinucleosome.bam 2018
4 IDR score
Finally, for the IDR score (for reproducibility) : is it something that can be extracted from the corr plot?