| | 1 | = v2.1.0 General info = |
| | 2 | |
| | 3 | Updated pipeline with new exon track, read more on the gitlab repository. |
| | 4 | |
| | 5 | == Gitlab repository == |
| | 6 | |
| | 7 | https://git.lumc.nl/rp3/RNA-seq-pipeline/commits/v2.1.0 |
| | 8 | |
| | 9 | == Sample count == |
| | 10 | |
| | 11 | Eventually all samples will be analyzed using this version. |
| | 12 | |
| | 13 | * Started out with 622 NTR samples. |
| | 14 | |
| | 15 | == Database == |
| | 16 | |
| | 17 | https://picas.grid.sara.nl:6984/_utils/database.html?rp3_analysis |
| | 18 | |
| | 19 | == Views == |
| | 20 | |
| | 21 | Several views are created and are ready to extract data from the database. |
| | 22 | |
| | 23 | ''' Outputs ''' |
| | 24 | |
| | 25 | To get a json object with all the locations of the output so far with |
| | 26 | pipeline v2.1.0 use curl to get the v210_outputs view: |
| | 27 | |
| | 28 | {{{ |
| | 29 | curl -X GET https://picas.grid.sara.nl:6984/rp3_analysis/_design/v2.1.0/_view/outputs -k -u username |
| | 30 | }}} |
| | 31 | |
| | 32 | ''' Statistics and QC ''' |
| | 33 | |
| | 34 | For the run statistics and qc use the 'statistics' view: |
| | 35 | |
| | 36 | {{{ |
| | 37 | https://picas.grid.sara.nl:6984/rp3_analysis/_design/v2.1.0/_view/statistics |
| | 38 | }}} |
| | 39 | |
| | 40 | == Issues == |
| | 41 | |
| | 42 | * 4 samples turned out to share 2 barcodes. Removed until re-sequenced. |
| | 43 | {{{ |
| | 44 | Resequenced: |
| | 45 | AD2D3NACXX-7-9 NTR08323 |
| | 46 | AD2D3NACXX-7-9 NT0027701 |
| | 47 | BC2B59ACXX-7-14 NTR05309 |
| | 48 | BC2B59ACXX-7-14 NTR09799 |
| | 49 | }}} |
