Dear all,

In attachment the result of mapping for 32-36bp length reads.

Most of the hits are to supercontigs.

Here is the possible explanation:

In alignments a lot of reads map to GL000220.1.
My colleague Mat Davis  found the following explanation online from Ian Dunham (Ensembl) regarding someone else's question:

 "In human the ribosomal RNA gene clusters containing the 28S, 18S and 5.8S RNAs are located on the short arms of the acrocentric chromosomes (13, 14, 15, 21 and 22) in long repeating arrays of 40 odd kb for a single unit. You have many copies in the arrays and copy number is variable between individuals. These regions are difficult to assemble into what are now called supercontigs because of this repeating structure and other satellite repeats that lie on these chromosome arms, so although there have been some BACs sequenced representing the clusters, the contigs are not integrated into the chromosome supercontigs. Instead they lie on the set of unplaced supercontigs. Supercontig GL000220.1 for instance is one of these. There are others. In the sequence databases there are several BACS that cover these clusters."

So it seems the mapping to rRNAs and to supercontigs is related.

Regards,
Natalja

    

    
 On
      2/23/12 11:37 AM, Tuuli Lappalainen wrote:
      

        
        Dear all, 

        

        We'll have our Geuvadis RNAseq analysis group call again today
        (Thursday) at 2pm. 

        

        Things to be discussed:

        - update on sequencing progress

        - miRNA QC issues

        - Tuuli will present some slides on how genetic variants affect
        mapability, and ways to correct for it

        - mRNA and miRNA data processing pipelines

        

        

        

        Call details: 

          
        

          
            

              
                
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                    91 495 18 99

              		
            

            

              
                
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        best regards, 

        Tuuli

        

        

        
-- 
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen@unige.ch

      

      

      

      

      
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-- 
Natalja Kurbatova, PhD
Functional Genomics Group, EBI