Dear all,

sorry if this question is not appropriate to this list, but if you are
using DEXSeq probably you used htseq to make exon count previously. While
making the counts using the python script available we saw that counts are
being attributted to regions overlaping 2 genes, that what we think it
means the counts corrseponding to IDs that have 2 or more ensembl ids. But
then the most weird thing is that the total is being much higher than the
number of reads aligned, id htseq counting reads in the individual genes
and also in the gene fusions? Below is a summary of the counts. Thanks in
advance for the help.

Kind regards,

Andreia

   HTseq isoform read count summary for DEXSeq NS_1  _ambiguous 0  _empty
5338242  _lowaqual 0  _notaligned 7690251  With feature 48284659  with
feature no overlap 43660100  with feature overlap 4624559  total 61313152



 sam file counts NS_1  Real Pair Number 43,324,075  against total DESeq
counts 260,581  against total DEXseq counts -17,989,077
-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

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