Hello,
I am new to using R and ChIP-seq analysis and I was having trouble generating ChIPQC report and hoping if anyone can help me trouble shoot this.
so what I did so far is
source("http://bioconductor.org/biocLite.R")
biocLite("BiocParallel")
biocLite("ChIPQC")
library(ChIPQC)
library(BiocParallel)
register(SerialParam())
> samples <- read.csv('jkim622_chipseq/meta/ChIPQC.csv')
> View(samples)
> chipObj <- ChIPQC(samples, annotation="hg19", chromosomes = NULL)
And below is what I got along with the error message at the end
E_Veh_1 MCF7 ERa 40min 1 narrow
E_Veh_2 MCF7 ERa 40min 2 narrow
E_Veh_3 MCF7 ERa 40min 3 narrow
E_2_1 MCF7 ERa 40min 1 narrow
E_2_2 MCF7 ERa 40min 2 narrow
E_2_3 MCF7 ERa 40min 3 narrow
E_3_1 MCF7 ERa 40min 1 narrow
E_3_2 MCF7 ERa 40min 2 narrow
E_3_3 MCF7 ERa 40min 3 narrow
E_4_1 MCF7 ERa 40min 1 narrow
E_4_2 MCF7 ERa 40min 2 narrow
E_4_3 MCF7 ERa 40min 3 narrow
Compiling annotation...
Using default blacklist for hg19...
Computing metrics for 24 samples...
list
Bam file has 195 contigs
Calculating coverage histogram for chr1
Calculating SSD for chr1
Calculating unique positions per strand for chr1
Calculating shift for chr1
300 / 300
Counting reads in features for chr1
Signal over peaks for chr1
done
Calculating coverage
Calculating coverage histogram for chr2
Calculating SSD for chr2
Calculating unique positions per strand for chr2
Calculating shift for chr2
300 / 300
Counting reads in features for chr2
Signal over peaks for chr2
done
Calculating coverage
Calculating coverage histogram for chr3
Calculating SSD for chr3
Calculating unique positions per strand for chr3
Calculating shift for chr3
300 / 300
Counting reads in features for chr3
Signal over peaks for chr3
done
Calculating coverage
Calculating Summits on chr3 ..Calculating coverage histogram for chr4
Calculating SSD for chr4
Calculating unique positions per strand for chr4
Calculating shift for chr4
300 / 300
Error: subscript contains out-of-bounds ranges
In addition: Warning messages:
1: In if is.na(peaks)) peaks = NULL :
the condition has length > 1 and only the first element will be used
2: In if is.na(blacklist)) blacklist = NULL :
the condition has length > 1 and only the first element will be used
Can someone tell me why I get an error? Also, how do I fix this?
Thank you all in advance for your help!
Ji
I know this is 4.5 years old. I encountered this problem because I had used hg38 to align my reads and I was using hg19 in thr CHIPQC() method. so changing the annotation to hg38 is the solution