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