ChIPQC 'Contigs of interest are not all in Bam file!!' error
0
1
Entering edit mode
Jonah • 0
@81aa349a
Last seen 7 weeks ago
United States

I have 6 samples, 3 sets of 2 replicates. Not sure why the error is coming up. Something that seems off is that it says 'computing metrics for 10 samples when I only have 6.

chipObj <- ChIPQC(samples, annotation="hg38")

The error is below.

Checking chromosomes:
[1] "1"
Compiling annotation...
Computing metrics for 10 samples...
list
Bam file has 195 contigs
Error in sampleQC(bamFile = reads, bedFile = peaks, GeneAnnotation = annotation,  : 
  Contigs of interest are not all in Bam file!!
In addition: Warning message:
In if (is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

Let me know if you need any other tests/outputs to help solve this!

Thanks!

ChIPQC • 95 views
ADD COMMENT
0
Entering edit mode

I realized I have the same control for 2 replicates of 2 factors, which makes the 10 number make sense: 6 experimental bams, 4 control bams. Does ChIPQC not support duplicate control files?

ADD REPLY

Login before adding your answer.

Traffic: 454 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6