AlgoLab/PIntron — Issue #11: Small exons not found
Author: yp
Created: 2011-12-19 11:31:15+00:00
State: open
Labels: bug

RefSeq [annotation](http://www.ncbi.nlm.nih.gov/nuccore/NM_001127) of transcript NM_001127 of gene AP1B1 presents a "small" exon (9nt) at position (1-based inclusive, relative to the transcript sequence) `2954..2962`, while PIntron factorizes the transcript as follows (last two exons):

2799 2962 92664 92825
2963 4178 94301 95516

(The last exon coincides with the reference annotation.)

PIntron version: `v1.2.25`
Input files: https://gist.github.com/14784a4ceec5e20f73d8
Command-line:

./bin/pintron --bin-dir=./bin/ -k --genomic=genomic.txt --EST=ests.txt --organism=human --gene=AP1B1 --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