Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Annotate contigs with BLAST hit names; remove contigs with no hit Bueller_007 Bioinformatics 10 02-27-2013 11:22 AM
GSMapper trimming Peitx Bioinformatics 6 10-10-2011 12:23 PM
Roche gsMapper output exon contigs rather than full-length sequence? sulicon Bioinformatics 0 02-28-2011 05:51 PM
gsMapper problem pcg 454 Pyrosequencing 2 12-06-2010 02:29 AM
Roche's gsMapper Layla 454 Pyrosequencing 6 09-16-2009 01:22 PM

Thread Tools
Old 01-22-2010, 12:15 PM   #1
Junior Member
Location: toronto canada

Join Date: Aug 2009
Posts: 5
Default gsMapper contigs

Hello All,

What does the lower case and upper case Letters in the contigs build by gsMapper represent?

Also, How is HCDiff (high confidence) variations differences determined?

haonmada is offline   Reply With Quote
Old 01-22-2010, 12:25 PM   #2
Location: Washington DC Metro Area

Join Date: Aug 2009
Posts: 20

Hi Ha,

The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants that have at least 3 non-duplicate reads relative to the reference or to other reads at that specific location.

I also found another thread that discusses uppercase and lower case and maybe helpful.
Justin H. Johnson | Twitter: @BioInfo | LinkedIn: | EdgeBio
jjohnson 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 03:00 AM.

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