Tandem Poly(A) sites' expression has been quantified with the PAQR tool
(
Gruber A.J. et al.).
Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table.
Each row in the expression table represents a single, unique Poly(A) site (PAS).
The first 10 columns contain the following information:
chrom : PAS chromosome
start : PAS start coordinate (BED format)
end : PAS end coordinate (BED format)
pas : PAS ID (as in the PAS annotation used)
score : score of the PAS annotation used
strand : PAS strand
polyAsite_exon_idx : PAS index on a specific terminal exon
nr_polyAsites_on_exon : total number of Poly(A) sites on a specific terminal exon
exon : unique terminal exon ID
gene : transcript ID of this specific terminal exon
Each of the next columns stores TPM values of
a specific RNA-Seq sample, as in the scheme below:
|
chrom |
start |
end |
pas |
score |
strand |
polyAsite_exon_idx |
nr_polyAsites_on_exon |
exon |
gene |
Sample1 |
Sample2 |
... |
| PAS1 |
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| PAS2 |
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| PAS3 |
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| ... |
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