DeepTools Error: Be sure that the bam files you are using is indexed.

Question

[dally]

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.

Answer 1

[matted]

You are giving it the index files (*.bam.bai), when you should probably be giving it the bam files (*.bam).

[dally]

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 pearson parameters. It keeps telling me that it is an unrecognized argument. But everything on the github has the parameters written exactly like this. Any ideas?

The --plotFile command appears to be unrecognized as well.

[matted]

I'm not sure. Maybe you have an old version installed?