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Old 01-09-2019, 10:54 AM   #1
Location: Oklahoma

Join Date: Jan 2012
Posts: 35
Default Deciding how many reads map to a plasmid or to a genome

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...

Last edited by fznajar; 01-09-2019 at 01:44 PM.
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