Hi Dave,
regarding BitSeq's non-uniform read distribution model. BitSeq learns 
two separate bias models for sense and anti-sense reads so these reads 
are being distinguished.

Kind regards,
Peter.

On 29/01/13 09:19, Dave Gerrard wrote:
> Hi Peter,
> Thanks for your reply.  A lot of 'conventional' cDNA protocols created 
> double-stranded DNA, from which the orginal strand information was 
> lost but some RNA based library protocols retain the strandedness (see 
> http://biology.stackexchange.com/questions/1958/difference-between-strand-specific-and-not-strand-specific-rna-seq-data 
> ).  The difference would matter most when you have overlapping 
> transcritps (common in small genomes) or you have no clue about 
> transcription strand (ncRNAs with no poly-A).
>
> However, given that I am working on poly-A extracted RNAs from the 
> sparse human genome, and BitSeq's mapping strategy, it's not too bad 
> an assumption that the coding strand was the source.
>
> The reason I asked was because Cufflinks refuses to do non-uniform 
> distribution without strand information (according to the manual).   
> From you answer, it sound's like BitSeq infers the strand from the 
> mapping direction (which is what I want) but does it then do something 
> different for reads that map in the anti-sense direction?
>
> Dave
>
>
> On 27 January 2013 20:37, Peter Glaus <glaus@cs.man.ac.uk 
> <mailto:glaus@cs.man.ac.uk>> wrote:
>
>     Hi Dave,
>     as far as I understand the RNA-seq protocols, the "endedness" of
>     reads is determined depending on whether they were generated in
>     first-strand synthesis or second-strand synthesis.
>
>     Either way, this can be also determined based on transcripts
>     "strandedness" (in our case known from annotation) and read being
>     aligned to sense or anti-sense strand of the transcript. So BitSeq
>     tries to determine end for each read and it is safe to use the
>     non-uniform model.
>
>     If you want to make sure that everything runs OK you can use
>     verbose flag to get more information and check the number of reads
>     that are reported in the pre-processing part and watch for any
>     unexpected warnings.
>
>     Regards,
>     Peter.
>
>
>
>     On 01/25/2013 12:02 PM, Dave Gerrard wrote:
>>     I have RNAseq data generated from poly-A capture RNAs.  There
>>     appears to be a strong 3' bias to the mapped reads but the
>>     library prep was NOT strand specifc. I would like to correct for
>>     the positional bias in the mapped reads and  Bitseq has a
>>     'uniform' parameter which can be set to 'FALSE' if reads are not
>>     uniform.  Please can you tell me if this requires 'stranded'
>>     mapped read information (as per the cufflinks manual) or whether
>>     It will work without knowing the source strand?
>>
>>     Thanks,
>>     Dave Gerrard
>>     -- 
>>     david.gerrard@manchester.ac.uk
>>     <mailto:david.gerrard@manchester.ac.uk>
>>
>>     Bioinformatics | The University of Manchester | Michael Smith
>>     Building | Room B.1079 | Oxford Road | Manchester | M13 9PT
>>     T: 0161 275 5737
>>
>>     http://personalpages.manchester.ac.uk/staff/David.Gerrard/ 
>
>
>
>
> -- 
> david.gerrard@manchester.ac.uk <mailto:david.gerrard@manchester.ac.uk>
>
> Bioinformatics | The University of Manchester | Michael Smith Building 
> | Room B.1079 | Oxford Road | Manchester | M13 9PT
> T: 0161 275 5737
>
> http://personalpages.manchester.ac.uk/staff/David.Gerrard/ 

	[[alternative HTML version deleted]]

