Mouse Reads and Human Reads Similarity

Question

[Ron]

Hi all,

This question is related to the post here:

Tool to separate human and mouse rna seq reads

I am using BBMAP for separating human and mouse reads.Here is the output of statistics :

 #Matched     95918464    100.92671%
 #Name  Reads   ReadsPct     Bases          BasesPct
  hg19  79591774    83.74754%   8038769174  83.74754%
 mm10   16326690    17.17916%   1648995690  17.17916%

I want to calculate human and mouse reads individual percentage(removing any similar reads between human and mouse, which are counted here)? As similar reads between mouse and human are also reported here(since the percentage also crosses 100% ). Any suggestions ?

Thanks,

Ron

Answer 1

[GenoMax]

Option to consider for bbsplit is ambig2. Choose an appropriate setting based on how you want to handle reads that map to one or both.

ambiguous2=<best>    Set behavior only for reads that map ambiguously to multiple different references.
                     Normal 'ambiguous=' controls behavior on all ambiguous reads;
                     Ambiguous2 excludes reads that map ambiguously within a single reference.
                     best   (use the first best site)
                     toss   (consider unmapped)
                     all   (write a copy to the output for each reference to which it maps)
                     split   (write a copy to the AMBIGUOUS_ output for each reference to which it maps)

ambig2=best is the default.