Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA Soft Clipping Bio.X2Y Bioinformatics 11 03-09-2015 09:08 AM
samtools mpileup floating point error Hkins552 Bioinformatics 12 03-02-2014 08:13 AM
Clipping adapters nsl RNA Sequencing 6 05-27-2011 02:08 PM
MosaikBuild entry point missing ursaan Bioinformatics 0 04-23-2010 06:08 AM
controlling clipping behavior in bwa 'aln' and 'bwtsw' aligners jnfass Bioinformatics 1 01-10-2010 01:49 PM

Thread Tools
Old 04-15-2009, 03:27 AM   #1
Location: València, Spain

Join Date: Apr 2009
Posts: 48
Default what's clipping point?

I'm working with de novo 454 data and , after a GS FLX asemmbly, I try to see the results with clview which works with .ace files and I can see something like the attachment file. The reads have right and left clip. What does it mean? I found anything about this clipping point. Can I change some value in order to improve the assembly?
Thank you very much!
Attached Images
File Type: png assembly1.png (64.4 KB, 38 views)
jordi is offline   Reply With Quote
Old 05-26-2009, 01:47 AM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

Reads are quality trimmed before assembly, the new start and stop are the left and right clipping points. Usually, the left (5') side is never trimmed (beyond the first four bases that are common for all reads).

Trim values can be changed using the sfffile command, check the manual.
flxlex is offline   Reply With Quote

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 07:51 PM.

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