wiki:BIOS_Pipeline/v2.1.0

Version 1 (modified by jamverlouw, 9 months ago) (diff)

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v2.1.0 General info

Updated pipeline with new exon track, read more on the gitlab repository.

Gitlab repository

https://git.lumc.nl/rp3/RNA-seq-pipeline/commits/v2.1.0

Sample count

Eventually all samples will be analyzed using this version.

  • Started out with 622 NTR samples.

Database

https://picas.grid.sara.nl:6984/_utils/database.html?rp3_analysis

Views

Several views are created and are ready to extract data from the database.

Outputs

To get a json object with all the locations of the output so far with pipeline v2.1.0 use curl to get the v210_outputs view:

curl -X GET https://picas.grid.sara.nl:6984/rp3_analysis/_design/v2.1.0/_view/outputs -k -u username

Statistics and QC

For the run statistics and qc use the 'statistics' view:

https://picas.grid.sara.nl:6984/rp3_analysis/_design/v2.1.0/_view/statistics

Issues

  • 4 samples turned out to share 2 barcodes. Removed until re-sequenced.
    Resequenced:
    AD2D3NACXX-7-9  NTR08323
    AD2D3NACXX-7-9  NT0027701
    BC2B59ACXX-7-14 NTR05309
    BC2B59ACXX-7-14 NTR09799