Sequencing Human/Mouse ATAC libraries together?

Question

[e.antunes]

Hi all,

I am a novice to this and currently preparing mouse and human ATAC libraries. All samples are on different barcodes and we want to compare these samples, so we think it's better to sequence (100 bp, paired end, HiSeq-X-Ten) everything together to get similar depth across all and reduce batch effects.

I'm unsure if this is a problem for the sequencer or for the analysis too? After read-trimming and FastQC check, when I go to align the samples with BWA-MEM or Bowtie2 for example, could I run one analysis and select for aligned human and mouse reads or do two separate runs targeted to 1 species to separate them out?

Any help / suggestions are much appreciated.

Thanks, Eric

Answer 1

[GenoMax]

As long as you use unique indexes for samples (dual indexes would be best), QC and then balance the libraries in the pool so the contents are more or less uniform, you can mix and sequence these together. Post-run demultiplexing will separate all of your samples into independent files on a per sample basis.