Question: Help with DeepTools
1
Entering edit mode

Hi All,

A reviewer of our paper wants us to show the input normalized read density for our ChIP-Seq data in the IGV browser shots we have in several of our figures. I would like to use bamCompare from deepTools to do this input normalization and output as a BW file which can be viewed in IGV. I can then update the figures with the log2 normalized track to satisfy the reviewer. I have installed deepTools on our system and have executed a commend but am getting an error. Could someone help me trouble shoot why deepTools bamCompare is not running? Here is the command and the error....

$ /Users/jwlandry2/Desktop/Bioinfor.Tools/deepTools/bin/bamCompare --bamfile1 MAC_BPTF_ChIP-Seq_Rep1+Rep2_Combined_Trimmomatic_NoDuplicate_MapQ10.1744779.sorted.bam --bamfile2 MAC_INPUT_ChIP-Seq_Combined_Trimmomatic_NoDuplicate_MapQ10_DownsampleRep1+Rep2.1741331.sorted.bam --binsize 25 --fragmentLength 200 --missingDataAsZero no --ratio log2 --scaleFactorsMethod SES -o log2ratioBPTFChIP_vs_Input.bw
Traceback (most recent call last):
  File "/Users/jwlandry2/Desktop/Bioinfor.Tools/deepTools/bin/bamCompare", line 8, in <module>
    from deeptools import writeBedGraph
ImportError: No module named deeptools

Thanks for your help...

jos

ADD COMMENTlinkeditmoderate 2.1 years ago landrjos • 10 • updated 2.1 years ago genomax 68k
Entering edit mode
1

from below line, it seems the script that is causing error is a python script and it is not able to find module by name "deeptools". Either the module exists and module path is not registered, or module doesn't exist. If it exists, but module path is not in your executable path, try to add it (in your shell profile). If it doesn't exist, try to install it.

from deeptools import writeBedGraph ImportError: No module named deeptools

See if you can manually install deeptools module. Try installing pip and run pip install deeptools if you are using python version <3. If your python version is above >3, install pip3 and run pip3 install deeptools. Probably it needs root/sudo/administrator privileges to install.

ADD REPLYlinkeditmoderate 2.1 years ago
cpad0112
11k
Entering edit mode
1

Recommended: python -m pip install deeptools to make sure you are using your default python installation (in case you have multiple, which is often a source of trouble)

ADD REPLYlinkeditmoderate 2.1 years ago
WouterDeCoster
39k

Login before adding your answer.

Powered by the version 2.0