UMI Project Notes

Pipeline respositories

SCons based UMI pipeline - https://gitlab.labmed.uw.edu/genetics/umi_pipeline
NextFlow based UMI pipeline - https://github.com/sheenams/umi_nextflow
(note NF pipeline also moved here: https://gitlab.labmed.uw.edu/genetics/umi_nextflow)

Helpful links

IDT Bioinformatics Workflow

Research runs

191212_NB0330_MiniOncoKAPA263R-MONCv1
200103_HA0717_MiniOncoKAPA266R-MONCv1
200213_NB0357_MiniOncoKAPA280R-MONCv1

Archival location for those runs

/mnt/disk16/genetics/archival/tgc_output/191212_NB0330_MiniOncoKAPA263R-MONCv1
/mnt/disk16/genetics/archival/tgc_output/200103_HA0717_MiniOncoKAPA266R-MONCv1
/mnt/disk16/genetics/archival/tgc_output/200213_NB0357_MiniOncoKAPA280R-MONCv1

Some data also is located here:

/mnt/disk16/genetics/MONC_FULL_DATA/

Analysis Locations

Larf: /home/genetics/analysis/TGC/191212_NB0330_MiniOncoKAPA263R-MONCv1
Larf: /home/genetics/analysis/TGC/200103_HA0717_MiniOncoKAPA266R-MONCv1

Working locations for 263R, 266R, 280R and related code

/mnt/disk10/users/sheenams/umi_nextflow/
/mnt/disk10/users/sheenams/umi_pipeline_nf/
/mnt/disk10/users/sheenams/ngstools-umi/

Sample Information

Sample_ID	Library prep notes
263R01_A01_MONCv1_NB0330	standard prep
263R02_B01_MONCv1_NB0330	standard prep
263R03_C01_MONCv1_NB0330	standard prep
263R04_D01_MONCv1_NB0330	standard prep
263R05_E01_MONCv1_NB0330	standard prep
263R06_F01_MONCv1_NB0330	standard prep
263R07_G01_MONCv1_NA12878_NB0330	standard prep
266R01-A01-MONCv1-NA12878	1/5 ligation into PCR (4ul)
266R02-B01-MONCv1	1/10 ligation into PCR (2ul)
266R03-C01-MONCv1	1/15 ligation into PCR (1.3ul)
266R04-D01-MONCv1	1/20 ligation into PCR (1ul)
266R05-E01-MONCv1	1/50 ligation into PCR (0.4ul)
280R01_A01_MONCv1_NB0357	1/5 ligation into PCR
280R02_B01_MONCv1_NB0357	1/5 ligation into PCR
280R03_C01_MONCv1_NB0357	1/5 ligation into PCR
280R04_D01_MONCv1_NB0357	20ul into PCR
280R05_E01_MONCv1_NB0357	20ul into PCR
280R06_F01_MONCv1_NB0357	20ul into PCR

Older UMI Data locations

see /mnt/disk10/users/sheenams/UMI-do-no-delete/ for runs:

180125_MA0337_MiniOnco165R-MONCv1
181001_NA0300_MiniOncoKAPA190R-MONCv1
190109_NA0318_MiniOncoKAPA207R-MONCv1-UMI
190121_NA0322_MiniOncoKAPA209R-MONCv1
180411_NA0261_MiniOncoKAPA165R-MONCv1
190109_NA0318_MiniOncoKAPA207R-MONCv1
190109_NA0318_MiniOncoKAPA207R-MONCv1-UMI-singletons