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Feature #487

closed

Show full PGP9 and PGP12 genomes on snp.med and GET-E

Added by Tom Clegg about 12 years ago. Updated over 11 years ago.

Status:
Closed
Priority:
High
Assigned To:
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
fixed
Story points:
-

Description

"I'd like to have PGP9 & PGP12 genomes processed and visible on snp.med and get-evidence sites as soon as possible, so we can review them. It's not blocking me from working on the paper, but I want to have as much time as possible for us to look over them and evaluate new variants as needed." (Madeleine)

Actions #1

Updated by Madeleine Ball about 12 years ago

For PGP9:

Aurora CO USA
female
cell line 21833
Incheon/PGP9
http://snp.med.harvard.edu/results/job/169

Can then hide (but use the photo): http://snp.med.harvard.edu/results/job/32

Actions #2

Updated by Tom Clegg about 12 years ago

PGP9 now points to http://snp.med.harvard.edu/results/job/169/Rosalynn_Gill

 update jobs set human=16,label='cell line 21833, Incheon/PGP9',public=1 where id=169;
 update jobs set public=0 where id=32;
Actions #3

Updated by Tom Clegg about 12 years ago

In evidence.oxf shell:

cd /home/get-evidence
cat public_html/config.php; mysqldump -ael -uevidence -p evidence >~/evidence-@date +%s@.sql
make update_genomes

In evidence.oxf mysql, remove links to previous data set (now that it is not listed as public on snp.med):

delete from variant_occurs where dataset_id='T/snp/32';
delete from datasets where dataset_id='T/snp/32';
Actions #4

Updated by Madeleine Ball about 12 years ago

gff for Henry Louis Gates Jr (aka PGP12) can be found at:

wsa2@orchestra:/groups/pgp/illumina/pgp12$ md5sum HLGjr-snp.gff
7b7bbb5cfd4cd1433d1859b7b3c12c63 HLGjr-snp.gff

Please process in Trait-o-matic and upload to GET-Evidence. Phenotype should be available soon. Cell-line identifiers should also be available soon.

Henry Louis Gates Jr.
Cambridge, Ma
male
cell line
PGP12
Illumina

Actions #5

Updated by Madeleine Ball about 12 years ago

wsa2@orchestra:/groups/pgp/illumina/pgp12$ md5sum HLGjr-snp.gff
7b7bbb5cfd4cd1433d1859b7b3c12c63 HLGjr-snp.gff

Abraham - uploaded it here:
Actions #7

Updated by Tom Clegg about 12 years ago

PGP12 is now listed on evidence.personalgenomes.org as well.

Actions #8

Updated by Tom Clegg about 12 years ago

Only remaining task is to choose a suitable image for PGP12.

Actions #9

Updated by Madeleine Ball about 12 years ago

I think the CC-licensed Wikipedia image is fine for now:
http://en.wikipedia.org/wiki/Henry_Louis_Gates

Actions #10

Updated by Tom Clegg about 12 years ago

  • Resolution set to fixed

OK, wikipedia image is up.

Actions #11

Updated by Ward Vandewege over 11 years ago

  • Project changed from 19 to GET-Evidence
  • Category deleted (GET-Evidence)
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