ChIPQC 'Contigs of interest are not all in Bam file!!' error
0
1
Entering edit mode
Jonah • 0
@81aa349a
Last seen 7 months 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 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 • 196 views
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?