Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa
Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat / bowtie mapping discrepancies vineeth_s Bioinformatics 3 06-10-2011 04:44 AM
Splitting fasta AND quality on masked sequence mucku Bioinformatics 3 12-15-2010 11:53 AM
bwa masked sequence? rand Bioinformatics 2 11-09-2009 06:02 AM
GS Mapper output to consed shows dimmed ends with good sequence? gaster 454 Pyrosequencing 0 05-11-2009 12:43 PM
In Sequence: Yale Team Uses an Illumina GA to Sequence Yeast Transcriptome; Finds Gre Newsbot! Illumina/Solexa 0 05-06-2008 02:02 PM

Thread Tools
Old 03-05-2009, 05:55 PM   #1
Location: adelaide

Join Date: Sep 2008
Posts: 43
Default why consed finds discrepancies with masked n sequence


I have just received our first Illumina data & I have assembled it into Consed. Then I searched for high quality discrepancies as am looking for variants.

But also in the list brought up it has discrepancies with 'n' (masked) sequence in the RefSeq.

Why would the program compare the sequences to regions of N's . I would have thought it would only be looking for differences between the 4 bases.

How can I screen these out to reduce my long list of discrepancies?

Thanks alig
alig is offline   Reply With Quote
Old 03-12-2009, 09:29 AM   #2
Location: San Diego

Join Date: Mar 2009
Posts: 26

If you're using Phrap/Consed you might want to think about using something like MAQ or similar programs as Phrep/Consed will not do well with short read sequencing (doesn't really do well on anything but sanger BAC re-sequencing/assembly without tweaking it a lot really). If you're working on de-novo stuff and don't have a reference try velvet or euler-sr.

basickler is offline   Reply With Quote
Old 03-12-2009, 10:54 AM   #3
Senior Member
Location: Berlin, DE

Join Date: May 2008
Posts: 628

Consed uses cross_match to align the reads (454,illumina) against a reference sequence,
phrap is not invoked. If you are "working" with the alignment, e.g. some kind of finishing, then
you are somewhat dependent on programs like consed.

But I agree that consed / cross_match is not doing that well on that, mainly because of the
problem mentioned and as well as it (still) lacks some proper consensus recalculation after
(short) reads have been aligned.

So if you're just looking for discrepancies, I'd also recommend programs like MAQ or
Mosaik Assembler (from the Marth Lab) which is well suited for SNP searches as well.

sklages is offline   Reply With Quote
Old 06-12-2009, 12:32 PM   #4
Senior Member
Location: USA

Join Date: Jan 2008
Posts: 482

cross match seems pretty sensitive to aligning short reads correctly. It is a matter of obtaining SNP calls from it and then compare.

The discrepancies reported by consed need to go through some sort of filtering to be able to get good quality snp calls.. anyone worked with this?

perhaps cross match mapped reads -> maq map format -> maq SNP calling?
bioinfosm 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 08:32 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO