Help with DeepTools

Question

[landrjos]

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

[cpad0112]

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.

[WouterDeCoster]

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)

[kennyday]

I've tried both pip and pip3 install and this error

ImportError: No module named deeptools.misc

Answer 1

[Devon Ryan]

You have an old installation that's getting picked up rather than the newer one you want. If you run python -c 'import deeptools; print(deeptools.__file__)' then you'll see the path to that you need to delete (remove the entire folder and any similarly named .pyc or .egg files in the parent directory).

Please note that it is much easier to install deepTools with conda.