[ensembl-dev] question about chain-net results in table 'genomic_align'

[Zhang Di]

Hi,

    Finally I got the compara pipeline for whole genome alignment to work.

    The results of RAW, CHAIN, and NET are all stored in table
'genomic_align' distinguished by different method_link_species_id.

    I found that the some records of CHAIN and NET, contain a few base
pairs belong to gap region of its scaffold.

e.g.


 mysql> select method_link_species_set_id, dnafrag_id, dnafrag_start,
dnafrag_end from genomic_align where dnafrag_id = 4465 and
dnafrag_start=486;
+----------------------------+------------+---------------+-------------+
| method_link_species_set_id | dnafrag_id | dnafrag_start | dnafrag_end |
+----------------------------+------------+---------------+-------------+
|                          2 |       4465 |           486 |         567 |
|                          3 |       4465 |           486 |         567 |
+----------------------------+------------+---------------+-------------+


while for the dnafrag_id = 4465 , in my core database it is scaffold_2621 ,
seq_region_id = 429785:

mysql> select * from assembly where asm_seq_region_id = 429785;
+-------------------+-------------------+-----------+---------+-----------+---------+-----+
| asm_seq_region_id | cmp_seq_region_id | asm_start | asm_end | cmp_start |
cmp_end | ori |
+-------------------+-------------------+-----------+---------+-----------+---------+-----+
|            429785 |            181573 |       488 |     717 |         1 |
    230 |  -1 |
|            429785 |            191688 |         1 |     419 |         1 |
    419 |   1 |
|            429785 |            220761 |       718 |    1086 |         1 |
    369 |   1 |
+-------------------+-------------------+-----------+---------+-----------+---------+-----+



the 420 - 487 interval is a gap.

Is this normal result of CHAIN-NET ?

It is quite annoying because I want to use the compara_db for low coverage
gene build, and It will complain:

EXCEPTION:
     Could not find sequence-level pieces for scaffold_2621/486-744

Best reguards

-- 
Zhang Di
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