Hi!
I want to use IDR on peaks file obtained using HMMRATAC pipeline.
From this pipeline, we obtained a list of peaks in gappedPeak format (score in the 13th column) with the highest the score the better the call.
How can I use IDR to find reproducibility between replicates?
How can I change the comuns the IDR uses to find the score, considering the highest the score the better the call?
The files are as follows:
chr1 630114 630158 HighCoveragePeak_0 . . 0 0 255,0,0 1 44 0 -1 -1 -1
I runned the following command:
idr --verbose --samples MKN74R2_sorted.bed MKN74R3_sorted.bed --input-file-type bed --rank 13 --output-file MKN74-idr --plot --log-output-file MKN74.idr.log
And obtained the following error:
/home/cjose/Software/anaconda3/bin/idr --verbose --samples MKN74R2_sorted.bed MKN74R3_sorted.bed --input-file-type bed --rank 13 --output-file MKN74-idr --plot --log-output-file MKN74.idr.log
Traceback (most recent call last):
File "/home/cjose/Software/anaconda3/bin/idr", line 4, in import('pkg_resources').run_script('idr==2.0.3', 'idr')
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 1463, in run_script
exec(code, namespace, namespace)
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in
idr.idr.main()
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 840, in main
merged_peaks, signal_type = load_samples(args)
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 732, in load_samples
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 732, in
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 56, in load_bed
raise ValueError("Invalid Signal Value: {:e}".format(signal))
ValueError: Invalid Signal Value: -1.000000e+00
Thank you in advance for your help.
Cheers,
Celina
Hi! I want to use IDR on peaks file obtained using HMMRATAC pipeline. From this pipeline, we obtained a list of peaks in gappedPeak format (score in the 13th column) with the highest the score the better the call. How can I use IDR to find reproducibility between replicates? How can I change the comuns the IDR uses to find the score, considering the highest the score the better the call?
The files are as follows: chr1 630114 630158 HighCoveragePeak_0 . . 0 0 255,0,0 1 44 0 -1 -1 -1
I runned the following command: idr --verbose --samples MKN74R2_sorted.bed MKN74R3_sorted.bed --input-file-type bed --rank 13 --output-file MKN74-idr --plot --log-output-file MKN74.idr.log
And obtained the following error: /home/cjose/Software/anaconda3/bin/idr --verbose --samples MKN74R2_sorted.bed MKN74R3_sorted.bed --input-file-type bed --rank 13 --output-file MKN74-idr --plot --log-output-file MKN74.idr.log Traceback (most recent call last): File "/home/cjose/Software/anaconda3/bin/idr", line 4, in
import('pkg_resources').run_script('idr==2.0.3', 'idr')
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 1463, in run_script
exec(code, namespace, namespace)
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in
idr.idr.main()
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 840, in main
merged_peaks, signal_type = load_samples(args)
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 732, in load_samples
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 732, in
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/home/cjose/Software/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 56, in load_bed
raise ValueError("Invalid Signal Value: {:e}".format(signal))
ValueError: Invalid Signal Value: -1.000000e+00
Thank you in advance for your help. Cheers, Celina