Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Ambiguous Nucleotides not compatible in SIFT shanon e Illumina/Solexa 0 11-10-2011 04:15 PM
SIFT on the command line lamasmi Bioinformatics 2 08-17-2010 09:32 AM
samtools rm ambiguous alignment EHC Bioinformatics 0 06-11-2010 08:50 AM
BWA 0.5 and 0.5.5 are in-compatible Seq1234 Bioinformatics 3 12-08-2009 06:41 AM
Cost of nucleotides colicoli General 3 01-26-2008 04:58 AM

Thread Tools
Old 11-29-2011, 03:32 PM   #1
shanon e
Junior Member
Location: Sacramento

Join Date: Nov 2011
Posts: 2
Default Ambiguous Nucleotides not compatible in SIFT

I used samtools pileup with data from an illumina RNA-seq dataset aligned with Tophat to hg19. It gave me some ambiguous nucleotides in the call base.
SIFT is unable to process the ambiguous nucleotides, so they've been left out of the analysis with SIFT.
Here is an example of my pileup:
chr1 881627 G R 62 62 60 65 ,$a$,$a,aa,,a,,,.aAaaaaAaaa,,aaaa,,aaaA.A,,,A,a.Aaaaaa,,,,a,.,..a,.^~,
chr1 887801 A R 228 228 60 53 G$G$g$..,,,,Gg.g,,gG..Ggg.Gg,ggG..GGG.GGG,gg,.,,,,,.,..^~T
chr1 990773 C T 48 124 60 20 TtTTTTTtttTTTtTtttt^~t

Has anyone found a way to process these ambiguous nucleotides in SIFT so that the information they do hold can be utilized?
In addition, can anyone clarify when it is appropriate to run SIFT with Zero-Based or First-Based?
shanon e 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 03:27 PM.

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