HI Ben,

Do not apologise, this is excellent guidance! I have been bumbling about with 
pile up and your explanation makes it much clearer. I did not use BWA but 
tophat instead so I'll give it a go with bwa and see if it makes a difference. 
I'm off to a virology conference next week so I'm not sure how much chance I'll 
get to work on it but many thanks again and once I do get my teeth into it I'm 
sure I'll have some more questions - especially on the stats front. On a 
related subject I am also looking at indels to see if the virus has hotspots 
for transcription errors that may reflect a deliberate attempt by the virus to 
modulate RNApolII function through secondary RNA structure interfering with 
polII fidelity (I have no other evidence for this, just a mad shot in the 
dark!). Have you ever looked at this either?

Best Wishes,
David

On 8 Apr 2011, at 05:08, Benjamin Dickins wrote:

> Hi David,
> I'm sorry for a slow response. Relatively recently I solved a problem a bit 
> like this and would be happy to share more information with you. If your 
> genome is small I think it makes sense to map to a reference and identify 
> variant sites. (In my opinion de novo assembly isn't needed - see below).
> 
> A basic approach is: groom FASTA file -> map with BWA -> filter SAM (uniquely 
> mapped reads only) -> SAM-to-BAM -> Generate pileup -> Filter pileup
> 
> This gives you a position-by-position summary relative to the reference. And 
> that last step is important and needs the most care: you can have it print 
> out differences total numbers of non-reference bases. I can share some 
> information about thresholding how many of these constitute significant 
> evidence that a non-reference base is actually there at that position 
> (basically I use a binomial distribution and ask whether the distribution of 
> ref/non-ref would occur by chance). Given that coverage of small genomes 
> tends to be high, your first question about determining the actual genome 
> sequence (or the quasispecies consensus if you prefer!) can be answered by 
> majority rules: i.e., a small script (or with tools under "Text Manipulation" 
> heading) to read off the base with the most support at each position and then 
> to test whether that base == base in reference nucleotide column.
> 
> It's probably also worth thinking about PCR duplicates (from library prep) as 
> these could be a significant source of error, but they are also tricky when 
> many reads will be identical anyway in the input DNA.
> 
> Feel free to get in touch with me if you need a bit more clarity and/or some 
> more specifics...
> 
> cheers,
> Ben
> 
> On Apr 4, 2011, at 9:55 PM, Anton Nekrutenko wrote:
> 
>>> From: David Matthews <d.a.matth...@bristol.ac.uk>
>>> Date: April 4, 2011 6:02:03 PM EDT
>>> To: galaxy-user@lists.bx.psu.edu
>>> Subject: [galaxy-user] Assemble a consensus genome from NGS data
>>> 
>>> Hi,
>>> 
>>> Does anyone know how to get a consensus genome from NGS data indicating the 
>>> percent variance at each nucleotide? I have a small virus genome with 
>>> manyfold coverage from my transcriptomic run. I'd like to know what the 
>>> transcriptome indicates is the actual genome plus get a feel for any 
>>> hotspots where there appears to be significant varience from the reference 
>>> sequence (i.e. because the reference is wrong or perhaps because of 
>>> frequent errors in that region due to RNA pol II having a problem 
>>> accurately transcribing the sequence).
>>> 
>>> Many thanks!
>>> 
>>> David
>>> 
>>> 
>>> ___________________________________________________________
>>> The Galaxy User list should be used for the discussion of
>>> Galaxy analysis and other features on the public server
>>> at usegalaxy.org.  Please keep all replies on the list by
>>> using "reply all" in your mail client.  For discussion of
>>> local Galaxy instances and the Galaxy source code, please
>>> use the Galaxy Development list:
>>> 
>>>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>>> 
>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>> 
>>>  http://lists.bx.psu.edu/
>> 
> 
> Benjamin Dickins
> Postdoctoral Researcher
> Center for Comparative Genomics and Bioinformatics
> The Pennsylvania State University
> ------------------------------------------------------------
> 302 Wartik Laboratory
> University Park, PA 16802, USA
> Cell/mobile: +1 814 777 1852
> Office tel: +1 814 863 2185
> Office fax: +1 814 865 9131
> Website: http://www.bendickins.net/
> Weblog: http://www.open.ac.uk/blogs/ideasblog/
> 

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to