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...