AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
What steps will reproduce the problem?
1. Look at probeset 2352152, overlapping with ENST00000271277
2. Look at probeset 3161639 with the transcript cluster annotation 3161566
What is the expected output? What do you see instead?
Both Exon 1.0 probesets should be included in the AltAnalyze human EnsMart62
database, but are missing. In the first case, it appears that there isa second
gene overlapping with this probeset region, possibly resulting in exclusion.
The entire overlapping exon (ENSE00001450658) is properly annotated in
ensembl/Hs_Ensembl_exon.txt, hence, the issue arises in the module
ExonArrayEnsemblRules.py (probably overlapping transcript cluster annotations).
3161639 aligns to an intron of ENSG00000107077 and should be considered a
"full" annotation. Although, it shares the same transcript cluster ID as exon
aligning probesets for this gene, other annotated intron aligning probesets
have more than 1 different transcript clsuters. Hence, it is probably excluded
due to multiple overlapping transcript clusters. Since both 3161639 and the
exon aligning probesets for this gene share the same transcript cluster, it
should be included.
Testing during the next Ensembl build (EnsMart 63) should be conducted with
these probesets to assess where they are excluded and resolve if possible.
Original issue reported on code.google.com by nsalomo...@gmail.com on 12 Jun 2011 at 7:57
nsalomonis
commented
4 years ago
Original issue reported on code.google.com by
nsalomo...@gmail.comon 12 Jun 2011 at 7:57