Dear Annotators,
I added the read counts prepared by EJ Osborne (UTAH, Richard Clark's
lab)
This is how the data was prepared:
1)
stage_expression_11_30_09.xls:
this file contains the gene expression levels for a given gene across
the four stages sampled in the Illumina RNA-seq experiment. This may be
useful for 1) looking at expression differences across stages of
development and 2) ensuring that your gene of interest is expressed at
reasonable levels. Gene expression levels were calculated as follows:
-76
base RNAseq reads were trimmed to 60 bases (allowed for more higher
quality reads to be created)
-these
reads were then mapped to the EMBL annotation file provided by the VIB
(Gent) for the latest release of the annotation (14/10/09)
-reads
were mapped so that only uniquely mapping reads to a gene model were
counted (this removes multiple mapping reads that would cross map in
the case of genes with recent paralogs, that would result in an
inflation of gene expression counts for a specific gene).
-read
counts were normalized by million reads mapped:
unique reads
mapping to gene model A/ ((sum of reads mapping)/1000000)
this
sort of normalization allows for better comparisons between flowcell
lanes where read counts will vary.
The data is available on the BOGAS page, as of this morning (CET) as a
histogram allowing easy comparison between the developmental stages of
the mite.
For visual reasons and in order to use the available space, I made use
of a dynamic scale. This means that the length of a bar between
different 2 genes is not necessarily comparable.
Hoover therefore over a bar to get the actual value for a stage and
compare the values this way. As values are in a very broad range,
having a fixed scale is not possible (or everything with
low-to-moderate expression would be compressed to the point of not
being visible anymore)
best regards
Stephane
--
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Stephane Rombauts Principal Scientific staff
Research group of Bioinformatics & Evolutionary Genomics
Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
strom@psb.vib-ugent.be http://www.psb.vib-ugent.be
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