SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Should I do any quality filtering in such a case? GloriaFu Bioinformatics 4 06-10-2011 11:51 AM
454 amplicon quality filtering JackieBadger Bioinformatics 10 03-16-2011 01:28 PM
Accepted practices of NGS quality filtering? gaffa Bioinformatics 7 11-17-2010 08:05 AM
Filtering on quality Farhat Bioinformatics 4 05-19-2010 06:24 AM
Quality filtering Farhat SOLiD 0 05-13-2010 11:42 PM

Reply
 
Thread Tools
Old 01-30-2012, 02:57 PM   #1
GSCHALLA
Junior Member
 
Location: United States

Join Date: Nov 2011
Posts: 1
Default 454 quality filtering

Hi All:
I am new to NGS work. I am currently working on de novo assembly of transcriptome. While working with 454 data I noticed that there are some bases in the filtered/trimmed read with areas where quality is less than the threshold used for trimming/filtering. Is is a common thing. If so how it can be worked out or justified during assembly. I am using some perlscripts for quality trimming. In assembly these bases are masked ( ie in lowercase letters).

Another question, in the 454Read Status file many of the reads are designated as singletons. Are these reads included in the AllContig file or isotig file?

Thanks in advance and I appreciate your help.


Can any one direct me to any of the literature that explains all these thing about assembly.
GSCHALLA is offline   Reply With Quote
Reply

Tags
454 low quality areas

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 03:53 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO