SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to eliminate reads that map to multiple places in genome ammoon Bioinformatics 7 08-23-2017 06:43 AM
Differential Expression: is it better to map reads to genome or transcriptome? dalesan Bioinformatics 26 04-22-2014 04:02 AM
Tophat RNASeq mapping - right reads map and left reads map 50% less airad22 Bioinformatics 2 08-14-2013 08:26 AM
How to map short reads to a distant genome? ynwh Illumina/Solexa 5 08-03-2011 06:56 AM
How to map 454 reads/contigs to a mitochondrial genome? fruktimport Bioinformatics 2 03-28-2011 11:35 AM

Reply
 
Thread Tools
Old 01-09-2019, 10:54 AM   #1
fznajar
Member
 
Location: Oklahoma

Join Date: Jan 2012
Posts: 29
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.
fznajar is offline   Reply With Quote
Old 01-09-2019, 03:09 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,846
Default

#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?
GenoMax is offline   Reply With Quote
Old 01-09-2019, 03:10 PM   #3
fznajar
Member
 
Location: Oklahoma

Join Date: Jan 2012
Posts: 29
Default

You are correct GenoMax. They are identical. Appreciate it.
Best
fznajar is offline   Reply With Quote
Old 01-29-2019, 12:39 PM   #4
seb567
Senior Member
 
Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

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".
seb567 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:04 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO