[BioMart Users] platform field is missing (ICGC mart)

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[BioMart Users] platform field is missing (ICGC mart)

Jorge Zamora-2
Hello,

I've realized that in our local ICGC mart we miss the 'platform' menu
when querying for CNSM in the advanced interface.

I made sure I didn't get any errors when generating the script to
generate the secondary data and when running martloader.

Should I expect a 'platform' on this table?
cnv__copy_number_somatic_mutation__dm;

Thanks.
Jorge

mysql> desc cnv__copy_number_somatic_mutation__dm;
+-----------------------------+-----------------+------+-----+---------+-------+
| Field                       | Type            | Null | Key | Default |
Extra |
+-----------------------------+-----------------+------+-----+---------+-------+
| cnv_id_key                  | int(1) unsigned | YES  | MUL | NULL    
|       |
| mutation_id                 | varchar(64)     | YES  |     | NULL    
|       |
| mutation_type               | varchar(64)     | YES  |     | NULL    
|       |
| validation_status           | varchar(32)     | YES  |     | NULL    
|       |
| gene_affected               | text            | YES  |     | NULL    
|       |
| transcript_affected         | text            | YES  |     | NULL    
|       |
| donor_id                    | varchar(32)     | YES  | MUL | NULL    
|       |
| diagnosis_id                | varchar(32)     | YES  | MUL | NULL    
|       |
| tumour_sample_id            | varchar(32)     | YES  | MUL | NULL    
|       |
| analysis_id                 | varchar(32)     | YES  | MUL | NULL    
|       |
| biobank_id                  | varchar(32)     | YES  |     | NULL    
|       |
| gender                      | varchar(6)      | YES  |     | NULL    
|       |
| vital_status                | varchar(16)     | YES  |     | NULL    
|       |
| age_at_diagnosis            | int(1)          | YES  |     | NULL    
|       |
| sample_type                 | varchar(32)     | YES  |     | NULL    
|       |
| sample_freezing_method      | varchar(32)     | YES  |     | NULL    
|       |
| percent_intact_tumour_cells | int(1)          | YES  |     | NULL    
|       |
+-----------------------------+-----------------+------+-----+---------+-------+
17 rows in set (0.00 sec)


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Re: [BioMart Users] platform field is missing (ICGC mart)

Junjun Zhang
Re: [BioMart Users] platform field is missing (ICGC mart) Hi Jorge,

That depends on whether you populated the ‘platform’ field in the CNSM primary input file with any actual values or just put –999 indicating data is not available. Martloader will drop any column that is empty for all rows.

Hope this helps,
Junjun



On 11-04-05 5:07 AM, "Jorge Zamora" <jazamora@...> wrote:

Hello,

I've realized that in our local ICGC mart we miss the 'platform' menu
when querying for CNSM in the advanced interface.

I made sure I didn't get any errors when generating the script to
generate the secondary data and when running martloader.

Should I expect a 'platform' on this table?
cnv__copy_number_somatic_mutation__dm;

Thanks.
Jorge

mysql> desc cnv__copy_number_somatic_mutation__dm;
+-----------------------------+-----------------+------+-----+---------+-------+
| Field                       | Type            | Null | Key | Default |
Extra |
+-----------------------------+-----------------+------+-----+---------+-------+
| cnv_id_key                  | int(1) unsigned | YES  | MUL | NULL   
|       |
| mutation_id                 | varchar(64)     | YES  |     | NULL   
|       |
| mutation_type               | varchar(64)     | YES  |     | NULL   
|       |
| validation_status           | varchar(32)     | YES  |     | NULL   
|       |
| gene_affected               | text            | YES  |     | NULL   
|       |
| transcript_affected         | text            | YES  |     | NULL   
|       |
| donor_id                    | varchar(32)     | YES  | MUL | NULL   
|       |
| diagnosis_id                | varchar(32)     | YES  | MUL | NULL   
|       |
| tumour_sample_id            | varchar(32)     | YES  | MUL | NULL   
|       |
| analysis_id                 | varchar(32)     | YES  | MUL | NULL   
|       |
| biobank_id                  | varchar(32)     | YES  |     | NULL   
|       |
| gender                      | varchar(6)      | YES  |     | NULL   
|       |
| vital_status                | varchar(16)     | YES  |     | NULL   
|       |
| age_at_diagnosis            | int(1)          | YES  |     | NULL   
|       |
| sample_type                 | varchar(32)     | YES  |     | NULL   
|       |
| sample_freezing_method      | varchar(32)     | YES  |     | NULL   
|       |
| percent_intact_tumour_cells | int(1)          | YES  |     | NULL   
|       |
+-----------------------------+-----------------+------+-----+---------+-------+
17 rows in set (0.00 sec)


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

_______________________________________________
Users mailing list
Users@...
https://lists.biomart.org/mailman/listinfo/users


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users