Deciding how many reads map to a plasmid or to a genome

[fznajar]

Hi all,
I have illumina genome reads for an E. coli a collaborator is studying. The prep used had a plasmid as well. I have two questions:

1) For the reads that match both (e.g. lacI gene), how can I tell which came from the plasmid and which came from the genome?
2) Should I normalize by dividing on the total reads per library or only the mapped reads in a library?

Thanks in advance...

[GenoMax]

#1 = Unless there is/are SNP's which are captured by that particular read you would not be able to tell where the read came from. I assume the sequence of the gene is otherwise identical?

[fznajar]

You are correct GenoMax. They are identical. Appreciate it.
Best

[seb567]

If you'are using "bwa sampe" for aligning, the documentation says:

Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.

I don't know if it is the case with "bwa mem" or with "bwa aln".