<div>Hi,</div><div><br></div><div> Finally I got the compara pipeline for whole genome alignment to work.</div><div><br></div><div> The results of RAW, CHAIN, and NET are all stored in table 'genomic_align' distinguished by different method_link_species_id.</div>
<div> </div><div> I found that the some records of CHAIN and NET, contain a few base pairs belong to gap region of its scaffold.</div><div><br></div><div>e.g.</div><div> </div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div> mysql> select method_link_species_set_id, dnafrag_id, dnafrag_start, dnafrag_end from genomic_align where dnafrag_id = 4465 and dnafrag_start=486;</div><div><div>+----------------------------+------------+---------------+-------------+</div>
</div><div><div>| method_link_species_set_id | dnafrag_id | dnafrag_start | dnafrag_end |</div></div><div><div>+----------------------------+------------+---------------+-------------+</div></div><div><div>| 2 | 4465 | 486 | 567 | </div>
</div><div><div>| 3 | 4465 | 486 | 567 | </div></div><div><div>+----------------------------+------------+---------------+-------------+</div></div></blockquote><div><br></div>
<div>while for the dnafrag_id = 4465 , in my core database it is scaffold_2621 , seq_region_id = 429785:</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div>mysql> select * from assembly where asm_seq_region_id = 429785;</div>
</div><div><div>+-------------------+-------------------+-----------+---------+-----------+---------+-----+</div></div><div><div>| asm_seq_region_id | cmp_seq_region_id | asm_start | asm_end | cmp_start | cmp_end | ori |</div>
</div><div><div>+-------------------+-------------------+-----------+---------+-----------+---------+-----+</div></div><div><div>| 429785 | 181573 | 488 | 717 | 1 | 230 | -1 | </div>
</div><div><div>| 429785 | 191688 | 1 | 419 | 1 | 419 | 1 | </div></div><div><div>| 429785 | 220761 | 718 | 1086 | 1 | 369 | 1 | </div>
</div><div><div>+-------------------+-------------------+-----------+---------+-----------+---------+-----+</div></div></blockquote><div><br></div><div><br></div><div>the 420 - 487 interval is a gap.</div><div><br></div><div>
Is this normal result of CHAIN-NET ?</div><div><br></div><div>It is quite annoying because I want to use the compara_db for low coverage gene build, and It will complain:</div><div><br></div><div>EXCEPTION:</div> Could not find sequence-level pieces for scaffold_2621/486-744<br clear="all">
<div><br></div><div>Best reguards</div><div><br></div>-- <br>Zhang Di<br>