SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
What tools can convert sequence file from tabular format to fasta format? yangjianhunt Bioinformatics 5 03-26-2014 01:48 PM
[PERL] Compare two sequences from fasta file frenchcookie Bioinformatics 3 12-17-2012 07:59 AM
Concatenating Sequences Within a single Fasta File cdlam Bioinformatics 3 12-04-2012 07:54 AM
delete sequences (fasta) from file ina-maria Bioinformatics 2 07-17-2012 12:04 AM
Align multiple sequences in tabular or fasta format pchiang Bioinformatics 7 07-01-2011 10:18 PM

Reply
 
Thread Tools
Old 07-30-2013, 06:46 PM   #1
ekgough
Junior Member
 
Location: Canada

Join Date: Jul 2013
Posts: 1
Default How can I tell if 454 PE sequences in fasta file format have already been separated?

Hi

I am new to bioinformatics and have never worked with 454 PE sequences before. I have 454 PE reads in fasta file format. The sequencing was done on the Roche 454 Titanium platform.

My understanding is that 454 results are stored in .sff files, from which sequence and quality data must be extracted.

Is it safe to assume, then, that if I have fasta files the forward and reverse ends have been separated already? I only have one file, not two.

Is it possible for the ends to still be joined in the fasta file? If so, how can I tell if the PE sequences have been separated already?

Can anyone suggest tools for doing the separation if I need to? I've found pyrocleaner and the NGS QC Toolkit, but I have no experience with either of them.

thanks!

E
ekgough is offline   Reply With Quote
Old 08-12-2013, 01:01 AM   #2
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

You can tell if you either have multiple files for the reads, one with the left end and one with the right end, and perhaps a file with unsplittable (shotgun) reads. Or the names of the sequences can tell you, something like /1 and /2, or read1 and read2, or left and right, or whatever the splitting tool uses. You can splitt using sff_extract, or the newbler program from 454/Roche (perform and assembly and set the '-tr' option on).
flxlex is offline   Reply With Quote
Old 08-12-2013, 01:50 AM   #3
rhinoceros
Senior Member
 
Location: sub-surface moon base

Join Date: Apr 2013
Posts: 372
Default

Why don't you just ask from whoever gave you the file?
rhinoceros is offline   Reply With Quote
Reply

Tags
454 pyrosequencing, bioinformatics

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 12:00 AM.


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