Entering edit mode
7.6 years ago
dally ▴ 210
I am attempting to use the bamCorrelate function of deeptools to find the reproducibility between two chip seq replicates.
I have used samtools index BAMFILE to index my files, but I am still running into this error so I must not be doing this correctly.
Here is the command I used for deeptools
bamCorrelate bins \ --bamfiles /Volumes/mydata/2015108/IDRM/2015_10_21_0/analysis_results/Sample_Pol_II_9_29/Alignments/Pol_II_9_29.mapped.rgid.sorted.filtered.dups_remove.bam.bai \ /Users/jonathanreeder/carlos-projects/Dropbox/ChIP-Seq/hg19/old_data/Sample_Pol-II-Chip-N20/Alignments/Pol-II-Chip.mapped.rgid.sorted.filtered.dups_remove.bam.bai \ -out pol-correlation
Here's the error:
Be sure that the bam file you areusing is indexed.
Ahh I see. I fixed that and was able to run the command line just fine. However, I can't seem to get it to work when running the
--corMethod pearsonparameters. It keeps telling me that it is an unrecognized argument. But everything on the github has the parameters written exactly like this. Any ideas?
--plotFilecommand appears to be unrecognized as well.
I'm not sure. Maybe you have an old version installed?