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Idea #10103

closed

Add 60+ CGI whole genomes to Lightning

Added by Abram Connelly over 9 years ago. Updated almost 9 years ago.

Status:
Closed
Priority:
Normal
Assigned To:
-
Target version:
-
Start date:
09/19/2016
Due date:
Story points:
-

Description

Convert all 60+ CGI whole genomes into FastJ and CGF, update the library and load them into the current prototype.

This will demonstrate the "N+1" feature of lightning.

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 #1

Updated by Abram Connelly over 9 years ago

Collection located at: 9c7028b9688f133c4831e4ad91f60c21+10097 .

To recompress and index:

bdir="." 

for x in `ls $bdir | egrep gz` ; do
  echo $x
  gff=`basename $x .gz`

  pigz -d $bdir/$x
  bgzip $bdir/$gff
  bgzip -r $bdir/$gff.gz
  tabix $bdir/$gff.gz

done
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 #2

Updated by Abram Connelly over 9 years ago

  • Status changed from New to In Progress
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 #3

Updated by Abram Connelly over 9 years ago

The FastJ files have been created and are located in a staging area on lightning-dev1. They are currently being uploaded to the umbrella project l7g data and should be under the 'cgi-1kg-gff-69' collection.

The library files are being generated now. Once completed, they'll need to be merged with the current library by appending any new entries to the end. Once the new library is created, the CGF will be able to be created.

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 #4

Updated by Tom Morris almost 9 years ago

Is this still In Progress? Who's it assigned to?

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 #5

Updated by Abram Connelly almost 9 years ago

  • Status changed from In Progress to Closed

These GFF files have been indexed and uploaded to Keep (cgf-cgi-1kg-69). The CGF files have been created (cgi-1kg-gff-69) along with the associated span and other tile library files (sglf, glf.2bitgz, glf.2bitbz2).

The previous version of the tile library without the extra 69 datasets have been saved under:

Unfortunately it looks like the FastJ was not saved for the 69 in the project. These can be recreated from the GFF or the CGF but haven't been stored explicitly.

All these collections are stored in the l7g Data project.

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