Question: ChIP seq: Trying to use ChIPQC to measure quality of reads
0
gravatar for aropri
7 months ago by
aropri50
aropri50 wrote:

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.

chip-seq • 431 views
ADD COMMENTlink modified 6 months ago • written 7 months ago by aropri50

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.
code_formatting

ADD REPLYlink written 7 months ago by _r_am31k
0
gravatar for aropri
6 months ago by
aropri50
aropri50 wrote:

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.

ADD COMMENTlink written 6 months ago by aropri50
0
gravatar for jared.andrews07
7 months ago by
jared.andrews077.9k
Memphis, TN
jared.andrews077.9k wrote:

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

ADD COMMENTlink written 7 months ago by jared.andrews077.9k

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.

ADD REPLYlink written 7 months ago by aropri50
0
gravatar for Rory Stark
6 months ago by
Rory Stark880
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark880 wrote:

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?

ADD COMMENTlink written 6 months ago by Rory Stark880

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

ADD REPLYlink written 6 months ago by aropri50
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