Hi,

Im trying to run cn.MOPS using multiple bam files of different breeds and while I can successfully run it by breed, when attempting to use all of them i get the following error:

Error in getReadCountsFromBAM(BAMFiles, refSeqName = readLines("/users/lbuggiotti/WGresRussia/cn.MOPS/Chr_list.txt"),  : 
  Targets in Header file of  /users/lbuggiotti/bamKorea/bam_NCBI/SRR1262755.bam  are not identical to the header of the file /users/lbuggiotti/bamKorea/A01.realigned.rmdup.bam !
In addition: Warning messages:
1: In sn == names(targets[[i]]) :
  longer object length is not a multiple of shorter object length
2: In sl == as.integer(targets[[i]]) :
  longer object length is not a multiple of shorter object length
Execution halted

I have checked the header of the above mentioned bam files and they are different, however i dont know how to change them in order to look alike and run all of them together. Some of the bam files have been downloaded from ncbi, however the reference genome used is the same in all of them.

I hope you can help me with the issue.

Thanks a lot for your time and support,

Laura