SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
FastQC Problem polsum Bioinformatics 8 11-04-2016 09:07 AM
Where is FastQC? sklages General 10 02-06-2012 12:46 AM
fastQC papori RNA Sequencing 3 02-04-2012 02:48 PM
Need help for FastQC results. Thanks!! byou678 Bioinformatics 18 08-23-2011 02:53 PM
Fastqc error Seq84 Bioinformatics 0 04-27-2011 08:22 AM

Reply
 
Thread Tools
Old 07-30-2010, 11:10 AM   #1
newbie25
Junior Member
 
Location: Canada

Join Date: Jul 2010
Posts: 3
Question fastqc with 454?

Hi, I'm new to bioinformatics and have just received my first 454 data set (YAY!) I have been told that fastqc is a great program for visualizing the quality of your data and getting a good summary but it seems to be only for illumina reads? Can I use it for 454 reads if I convert them to fastq?
Thanks in advance!
newbie25 is offline   Reply With Quote
Old 07-06-2011, 08:12 PM   #2
raonyguimaraes
Member
 
Location: Belo Horizonte - Brazil

Join Date: Jun 2010
Posts: 38
Default

Yes you can! Here is an example of a report:

http://www.bioinformatics.bbsrc.ac.u...qc_report.html

I'm trying to find a real good example, like this one for Illumina, anyone ?

http://www.bioinformatics.bbsrc.ac.u...qc_report.html
raonyguimaraes is offline   Reply With Quote
Old 07-07-2011, 12:22 AM   #3
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

If someone has a good 454 dataset they'd be prepared to share (or even point to in SRA) then I'm happy to expand the list of example reports on the FastQC homepage. I'm actually working on a more systematic analysis of public data with the tool but I'm happy to put up more examples in the short term if people would find that useful.
simonandrews is offline   Reply With Quote
Old 07-07-2011, 12:52 PM   #4
raonyguimaraes
Member
 
Location: Belo Horizonte - Brazil

Join Date: Jun 2010
Posts: 38
Default

Hi Simon, thanks for you reply.

I got a similar report of my reads from 454 with the example you are providing on your website.

I would like to know what are the recommended tools to trim my reads based on the quality of my initial report. Them I could make the before/after report and test if this is really helping to improve my assembly and annotation in someway.

I know I can do this with some scripts in python or perl but I would like something more ready2go.

Found this tool that looks promising: http://bioinf.comav.upv.es/ngs_backbone/cleaning.html

What are your suggestions for this trimming before the assembly?
raonyguimaraes 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 07:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO