ngsplot flat lines as output

Question

[Sadia]

Hello, I've been trying to run ngsplot for a new ChIP-seq experiment, but I keep getting flat lines and empty heatmaps even when I use mulitple different input peak files. I re-ran the same code with the files from our older ChIP-seq experiment peak files and those work fine. Anyone have any ideas about why this might be happening?

My code: ngs.plot.r -G mm9 -R bed -C config.txt -O outputfilename

config.txt file: K8a_R1.nodups.bam inputfile “K8a” K8b_R1.nodups.bam inputfile “K8b”

First few lines of input file:

chr1 6270232 6270233 chr1:6269512-6270951 chr1 6278114 6278115 chr1:6277649-6278578 chr1 6296974 6296975 chr1:6296578-6297369 chr1 6444425 6444426 chr1:6444003-6444846 chr1 9197557 9197558 chr1:9197212-9197901

[Sadia]

chr1 6270232 6270233 chr1:6269512-6270951

chr1 6278114 6278115 chr1:6277649-6278578

chr1 6296974 6296975 chr1:6296578-6297369

chr1 6444425 6444426 chr1:6444003-6444846

chr1 9197557 9197558 chr1:9197212-9197901

Answer 1

[Sadia]

It turns out I had two peaks in the file starting with chr1_random. The program was able to run after I deleted those two rows.

[szp770]

hi, what do you mean by "chr1_random"