<div dir="ltr"><div>Dear developers </div><div><br></div><div>I have a script that I wrote (in attachment)  that gets me the refseq exons for give input gene </div><div><br></div><div>However when I use this code using the gene ASXL1 as an example is:<br></div><div><br></div><div><a href="http://test_query.pl">test_query.pl</a> ASXL1<br></div><div><br></div><div><div>QueryName<span class="" style="white-space:pre">   </span>feature_type<span class="" style="white-space:pre">      </span>common_name<span class="" style="white-space:pre">       </span>Biotype<span class="" style="white-space:pre">   </span>id<span class="" style="white-space:pre">        </span>chr<span class="" style="white-space:pre">       </span>start<span class="" style="white-space:pre">     </span>end<span class="" style="white-space:pre">       </span>strand</div><div>ASXL1<span class="" style="white-space:pre">        </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_001164603.1.1<span class="" style="white-space:pre">  </span>chr20<span class="" style="white-space:pre">     </span>30946147<span class="" style="white-space:pre">  </span>30946635<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_001164603.1.2<span class="" style="white-space:pre">  </span>chr20<span class="" style="white-space:pre">     </span>30954187<span class="" style="white-space:pre">  </span>30954269<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_001164603.1.3<span class="" style="white-space:pre">  </span>chr20<span class="" style="white-space:pre">     </span>30955530<span class="" style="white-space:pre">  </span>30955532<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_001164603.1.4<span class="" style="white-space:pre">  </span>chr20<span class="" style="white-space:pre">     </span>30956818<span class="" style="white-space:pre">  </span>30956926<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.5<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>31015931<span class="" style="white-space:pre">  </span>31016051<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.6<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>31016128<span class="" style="white-space:pre">  </span>31016225<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.7<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>31017141<span class="" style="white-space:pre">  </span>31017234<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.8<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>31017704<span class="" style="white-space:pre">  </span>31017856<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.9<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>31019124<span class="" style="white-space:pre">  </span>31019287<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.10<span class="" style="white-space:pre">    </span>chr20<span class="" style="white-space:pre">     </span>31019386<span class="" style="white-space:pre">  </span>31019482<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.11<span class="" style="white-space:pre">    </span>chr20<span class="" style="white-space:pre">     </span>31020683<span class="" style="white-space:pre">  </span>31020788<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.12<span class="" style="white-space:pre">    </span>chr20<span class="" style="white-space:pre">     </span>31021087<span class="" style="white-space:pre">  </span>31021720<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.13<span class="" style="white-space:pre">    </span>chr20<span class="" style="white-space:pre">     </span>31022235<span class="" style="white-space:pre">  </span>31027122<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div></div><div><br></div><div><br></div><div>As you can see, I am missing some of the exons for transcript NM_015338.5</div><div>In this case, the 1st 3 exons of transcript  NM_015338.5 are identical to NM_001164603.1, but I would expect to have them listed as :</div><div><br></div><div><div>ASXL1<span class="" style="white-space:pre">       </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.1<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>30946147<span class="" style="white-space:pre">  </span>30946635<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.2<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>30954187<span class="" style="white-space:pre">  </span>30954269<span class="" style="white-space:pre">  </span>+<span class="" style="white-space:pre"> </span></div><div>ASXL1<span class="" style="white-space:pre">      </span>Exon<span class="" style="white-space:pre">      </span>ASXL1<span class="" style="white-space:pre">     </span>protein_coding<span class="" style="white-space:pre">    </span>NM_015338.5.3<span class="" style="white-space:pre">     </span>chr20<span class="" style="white-space:pre">     </span>30955530<span class="" style="white-space:pre">  </span>30955532<span class="" style="white-space:pre">  </span>+</div></div><div><br></div><div>Can you tell me what is wrong with my approach and how I can retrieve the missing data?</div><div><br></div>Best regards
<div><br></div><div>Duarte</div></div>