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:
Spain
902 125 136
Other countries
+34 91 495 18 99
Participants' Pin-code:
764989*
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(a)unige.ch
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--
Natalja Kurbatova, PhD
Functional Genomics Group, EBI