ChIP seq: Trying to use ChIPQC to measure quality of reads

Question

[mropri]

I am using ChIPQC to get quality metrics of my reads. I have .bam files and .narrowpeaks files. I created a sample csv file called sample1.csv. The sample.csv sheet can be found at this link.

https://docs.google.com/spreadsheets/d/12sovnIbEyH8CF8kRml7B6NLWt8z-Ck-iykBHvBe5Uqg/edit#gid=589685588

My code is the following:

> samples <- read.csv('sample1.csv')
> View(samples)
> chipObj <- ChIPQC(samples, annotation="hg38")

However, I keep getting this error:

Error in if file.info(peaks)$size > 0) { : 
  missing value where TRUE/FALSE needed

Hope someone can help. I really would appreciate it.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[mropri]

I figured it out. The peak files I had generated needed to have the prefix "chr" before the chromosome number. So before it would be just 1, 2,3,......,X,Y. After the change it is chr 1, chr 2, chr 3............ chr X, chr Y. Thanks for all your help guys. If anyone is having a similar issue please message me, would love to help out.

Answer 2

[jared.andrews07]

One of your peaks files contains no peaks, potentially due to poor ChIP enrichment or other issues with peakcalling.

[mropri]

Thank you for answering. Are you sure because i checked my peak files and they all have about 20,000 peaks. I appreciate your help, do you think it could be my sample file and it is not formatted correctly.

Answer 3

[Rory Stark]

It would help to see your sample sheet sample1.csv.

The most common source of this error is the format of the peaks files not matching what is specified in the PeakCaller column. What is the type of the peak files, and what is specified in the sample sheet?

[mropri]

Thank you for answering, my sample.csv link is below, you should be able to access it: I appreciate your help in this very much.

https://docs.google.com/spreadsheets/d/12sovnIbEyH8CF8kRml7B6NLWt8z-Ck-iykBHvBe5Uqg/edit#gid=589685588