SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie2: Merged alignments to split reference /= aligning to whole reference? helloxine Bioinformatics 0 08-04-2014 11:18 AM
Cuffcompare : Reference or Merged transcriptome vramnarine RNA Sequencing 0 05-23-2014 12:54 PM
Comparing location of reads mapping to reference genome alyamahmoud RNA Sequencing 1 02-06-2014 06:10 AM
comparing results from two different reference genomes BAJ Bioinformatics 2 02-24-2009 07:38 AM

Reply
 
Thread Tools
Old 05-01-2015, 10:11 AM   #1
lcmb
Junior Member
 
Location: Bethesda, MD

Join Date: May 2015
Posts: 6
Default Comparing Merged Seqs to a Reference Seq

Hello,

I recently received paired-end reads from an amplicon library I sequenced with Illumina. I used BBMerge to merge the paired-ends and, now, I would like to compare my merged sequences to a reference. My goal is to analyze where the merged sequence may differ from the reference.

I have tried to write a small Perl program, but I am continually running into problems. I study DNA repair and, essentially, I would like to compare my merged sequences to the reference so that I may better understand repair efficiency.

Is anyone aware of any programs/scripts that could help me reach my goal of comparing my merges to a reference? They are about 200bp long. Thank you!
lcmb is offline   Reply With Quote
Old 05-01-2015, 10:16 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,745
Default

BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.

Added: Is your reference 200 bp long?
GenoMax is offline   Reply With Quote
Old 05-01-2015, 10:24 AM   #3
lcmb
Junior Member
 
Location: Bethesda, MD

Join Date: May 2015
Posts: 6
Default

Quote:
Originally Posted by GenoMax View Post
BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.

Added: Is your reference 200 bp long?
Yes, it is. Thank you, GenoMax! Will BBMap allow me to set any criteria for the alignment? For example, if I did not want any sequences that differ by more than 10% from my reference.
lcmb is offline   Reply With Quote
Old 05-01-2015, 10:35 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,745
Default

Run bbmap.sh on its own to see all the command line options.

Here are some relevant options

Quote:
Post-Filtering Parameters:

idfilter=0 Independant of minid; sets exact minimum identity
allowed for alignments to be printed. Range 0 to 1.
subfilter=-1 Ban alignments with more than this many substitutions.
insfilter=-1 Ban alignments with more than this many insertions.
delfilter=-1 Ban alignments with more than this many deletions.
indelfilter=-1 Ban alignments with more than this many indels.
editfilter=-1 Ban alignments with more than this many edits.
inslenfilter=-1 Ban alignments with an insertion longer than this.
dellenfilter=-1 Ban alignments with a deletion longer than this.

Last edited by GenoMax; 05-01-2015 at 10:37 AM.
GenoMax is offline   Reply With Quote
Old 05-01-2015, 10:42 AM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,745
Default

You could also convert your reads to fasta format (use reformat.sh from BBMap) and then use blat for the alignments.

Once you identify the reads that align I suppose you want to do a multiple sequence alignment?
GenoMax is offline   Reply With Quote
Reply

Tags
amplicon sequencing, bbmerge, illumina, paired end, sequence

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 06:09 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO