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Hello,<br>
I am using Ensembl API version 65 to obtain a 1000bp slice for each
gene for promoter content analysis. Basically my script uses the
start position of each gene and expands by a 1000bp from the 5' end
of a gene using co-ordinates obtained from the
"fetch_by_gene_stable_id()" method. On the plus strand this would be
a 1000bp upstream from the 5' end on a gene (the first UTR / exon).
My conceptual difficulties are :<br>
<br>
1) Does this orientation hold / differ for genes on the negative
strand? <br>
<br>
2) Do I need to reverse this when obtaining a slice from a gene
located on the negative strand i.e instead of obtaining a 1000bp
using the start co-ordinates I should use the end co-ordinates
obtained by the "fetch_by_gene_stable_id()" method? <br>
<br>
The reason I am confused is that the API documentation states :<br>
"Note that for historical reasons the
<kbd>fetch_by_gene_stable_id()</kbd> method always returns a slice
on
the forward strand even if the gene is on the reverse strand."<br>
<br>
Does this mean that all 5' slices obtained for genes using
co-ordinates from this method would ideally capture the
transcription start site regardless of strand orientation?<br>
<br>
Another portion of the API documentation states :<br>
<br>
"Like all Ensembl features the start of an exon is always less than
or
equal to the end of the exon, regardless of the strand it is on.
The start of the transcript is the start of the first exon of a
transcript on the forward strand or the end of the last exon of a
transcript on the reverse strand.
The start and end of a gene are defined to be the lowest start value
of
its transcripts and the highest end value respectively.
"<br>
<br>
Thank you,<br>
<br>
Sumir<br>
<br>
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