AlgoLab/PIntron — Issue #7: Wrong alignment of RefSeq sequence
Author: yp
Created: 2011-12-13 16:58:32+00:00
State: open

In the gene ABO, the factorization of RefSeq NM_020469 (gene ABO) computed by PIntron is composed by 8 exons, while the [reference annotation](http://www.ncbi.nlm.nih.gov/nuccore/NM_020469) is composed by 7 exons.
In particular, the last exon of the reference annotation is:

400 1580

while PIntron computes the following two exons:

400 1486 19730 20816
1487 1573 20897 20983

The factorization of the reference annotation achieves better sequence coverage with less exons and should be preferred.

PIntron version: `v1.2.21`
Input files: https://gist.github.com/de4e511243964902ae83
Command-line:

./bin/pintron --bin-dir=./bin/ -k --genomic=genomic.txt --EST=ests.txt --organism=human --gene=ABO --output=pintron-full-output.json --gtf=pintron-cds-annotated-isoforms.gtf --extended-gtf=pintron-all-isoforms.gtf --logfile=pintron-pipeline-log.txt --general-logfile=pintron-log.txt