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.