SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Ion Torrent versus 454 FLX Junior rubenken The Pipeline 6 07-24-2012 04:29 AM
Workshops and training programs: online or in-person for the 454 Junior RubyTuesday 454 Pyrosequencing 0 10-26-2011 12:00 PM
questions on ssaha2 pengchy Bioinformatics 0 09-25-2011 01:42 AM
Roche GS Junior mini 454 coming 2010 DSB 454 Pyrosequencing 12 06-16-2011 01:29 AM
ssaha2/ssahaET/smalt options for 454 titanium reads? eni Bioinformatics 0 04-07-2010 11:13 AM

Reply
 
Thread Tools
Old 05-13-2011, 09:22 AM   #1
jtrivino
Junior Member
 
Location: Valencia

Join Date: Feb 2011
Posts: 4
Default ssaha2 with 454 Junior

Hi

I want to align my 454 Junior dataset with ssaha2.My command shell is:

/share/apps/ssaha2_v2.5.3_x86_64/ssaha2 -rtype 454 -output sam -outfile MID2/454Reads.MID2.sam -save hg19 MID2/454Reads.MID2.fastq

In the Sam output many of the reads have 255 quality value, so haven't any report of quality value. Then I do a Indels calling and I can't see any indels because I lost many informations....

How I can process that values ​​quality? Why those value?

Thanks
jtrivino 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 02:50 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO