Filtering RNAseq data of one sample from two different species

Question

[arturo.marin]

Hi,

I have data from cells culture. In this culture there is two different species of mammal. This is caused by the technique to obtain stem cells. Is there some specific software or way to filtering the data from one of the species and do the RNAseq analysis with the rest of the data?

[arturo.marin]

Hi GeneMax, your solution worked fine. Thanks.

Answer 1

[GenoMax]

Use bbsplit.sh from BBmap suite with reference genomes for both organisms to bin the data. See the answer (and links in it) here: A: Extracting contaminated reads from the sequenced data . You will need to pay special attentions to ambiguous2= parameter to decide what to do with reads that bin to both genomes. You may want to keep them in 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)

[arturo.marin]

Hi GenoMax, I will try your solution with BBmap. Thanks.