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

fznajar · 01-09-2019, 10:54 AM

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 · 01-09-2019, 03:09 PM

#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 · 01-09-2019, 03:10 PM

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

seb567 · 01-29-2019, 12:39 PM

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

Quote:

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".

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01-09-2019, 10:54 AM	#1
fznajar Member Location: Oklahoma Join Date: Jan 2012 Posts: 35	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.

01-09-2019, 03:09 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	#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?

01-09-2019, 03:10 PM	#3
fznajar Member Location: Oklahoma Join Date: Jan 2012 Posts: 35	You are correct GenoMax. They are identical. Appreciate it. Best