Setup¶
Pre-Setup¶
SampleSheet.csv¶
You will need to ensure that a SampleSheet is present at the top level of the folder holding the bcl files in your project’s Google bucket. A working SampleSheet.csv is shown below. The demultiplexing should work if you follow this format. Note that the only columns that are strictly necessary (to our knowledge) are sample_id, sample_name, and index.
SampleSheet.csv¶[Data],,,,,,,
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2
1,WT1_Th0_1,,A1,N701,TAAGGCGA,S502,ATAGAGAG
2,WT1_Th0_2,,B1,N701,TAAGGCGA,S503,AGAGGATA
3,WT2_Th0_1,,C1,N701,TAAGGCGA,S504,TCTACTCT
4,WT2_Th0_2,,D1,N701,TAAGGCGA,S505,CTCCTTAC
5,WT3_Th0_1,,E1,N701,TAAGGCGA,S506,TATGCAGT
6,WT3_Th0_2,,F1,N701,TAAGGCGA,S507,TACTCCTT
7,KO1_Th0_1,,A2,N702,CGTACTAG,S502,ATAGAGAG
8,KO1_Th0_2,,B2,N702,CGTACTAG,S503,AGAGGATA
9,KO2_Th0_1,,C2,N702,CGTACTAG,S504,TCTACTCT
10,KO2_Th0_2,,D2,N702,CGTACTAG,S505,CTCCTTAC
11,KO3_Th0_1,,E2,N702,CGTACTAG,S506,TATGCAGT
12,KO3_Th0_2,,F2,N702,CGTACTAG,S507,TACTCCTT
13,WT1_Th1_1,,A3,N703,AGGCAGAA,S502,ATAGAGAG
14,WT1_Th1_2,,B3,N703,AGGCAGAA,S503,AGAGGATA
15,WT2_Th1_1,,C3,N703,AGGCAGAA,S504,TCTACTCT
16,WT2_Th1_2,,D3,N703,AGGCAGAA,S505,CTCCTTAC
17,WT3_Th1_1,,E3,N703,AGGCAGAA,S506,TATGCAGT
18,WT3_Th1_2,,F3,N703,AGGCAGAA,S507,TACTCCTT
19,KO1_Th1_1,,A4,N704,TCCTGAGC,S502,ATAGAGAG
20,KO1_Th1_2,,B4,N704,TCCTGAGC,S503,AGAGGATA
21,KO2_Th1_1,,C4,N704,TCCTGAGC,S504,TCTACTCT
22,KO2_Th1_2,,D4,N704,TCCTGAGC,S505,CTCCTTAC
23,KO3_Th1_1,,E4,N704,TCCTGAGC,S506,TATGCAGT
24,KO3_Th1_2,,F4,N704,TCCTGAGC,S507,TACTCCTT
25,WT1_Th17n_1,,A5,N705,GGACTCCT,S502,ATAGAGAG
26,WT1_Th17n_2,,B5,N705,GGACTCCT,S503,AGAGGATA
27,WT2_Th17n_1,,C5,N705,GGACTCCT,S504,TCTACTCT
28,WT2_Th17n_2,,D5,N705,GGACTCCT,S505,CTCCTTAC
29,WT3_Th17n_1,,E5,N705,GGACTCCT,S506,TATGCAGT
30,WT3_Th17n_2,,F5,N705,GGACTCCT,S507,TACTCCTT
31,KO1_Th17n_1,,A6,N706,TAGGCATG,S502,ATAGAGAG
32,KO1_Th17n_2,,B6,N706,TAGGCATG,S503,AGAGGATA
33,KO2_Th17n_1,,C6,N706,TAGGCATG,S504,TCTACTCT
34,KO2_Th17n_2,,D6,N706,TAGGCATG,S505,CTCCTTAC
35,KO3_Th17n_1,,E6,N706,TAGGCATG,S506,TATGCAGT
36,KO3_Th17n_2,,F6,N706,TAGGCATG,S507,TACTCCTT
37,WT1_Th17p_1,,A7,N707,CTCTCTAC,S502,ATAGAGAG
38,WT1_Th17p_2,,B7,N707,CTCTCTAC,S503,AGAGGATA
39,WT2_Th17p_1,,C7,N707,CTCTCTAC,S504,TCTACTCT
40,WT2_Th17p_2,,D7,N707,CTCTCTAC,S505,CTCCTTAC
41,WT3_Th17p_1,,E7,N707,CTCTCTAC,S506,TATGCAGT
42,WT3_Th17p_2,,F7,N707,CTCTCTAC,S507,TACTCCTT
43,KO1_Th17p_1,,A8,N708,CAGAGAGG,S502,ATAGAGAG
44,KO1_Th17p_2,,B8,N708,CAGAGAGG,S503,AGAGGATA
45,KO2_Th17p_1,,C8,N708,CAGAGAGG,S504,TCTACTCT
46,KO2_Th17p_2,,D8,N708,CAGAGAGG,S505,CTCCTTAC
47,KO3_Th17p_1,,E8,N708,CAGAGAGG,S506,TATGCAGT
48,KO3_Th17p_2,,F8,N708,CAGAGAGG,S507,TACTCCTT
49,WT1_Treg_1,,A9,N709,GCTACGCT,S502,ATAGAGAG
50,WT1_Treg_2,,B9,N709,GCTACGCT,S503,AGAGGATA
51,WT2_Treg_1,,C9,N709,GCTACGCT,S504,TCTACTCT
52,WT2_Treg_2,,D9,N709,GCTACGCT,S505,CTCCTTAC
53,WT3_Treg_1,,E9,N709,GCTACGCT,S506,TATGCAGT
54,WT3_Treg_2,,F9,N709,GCTACGCT,S507,TACTCCTT
55,KO1_Treg_1,,A10,N710,CGAGGCTG,S502,ATAGAGAG
56,KO1_Treg_2,,B10,N710,CGAGGCTG,S503,AGAGGATA
57,KO2_Treg_1,,C10,N710,CGAGGCTG,S504,TCTACTCT
58,KO2_Treg_2,,D10,N710,CGAGGCTG,S505,CTCCTTAC
59,KO3_Treg_1,,E10,N710,CGAGGCTG,S506,TATGCAGT
60,KO3_Treg_2,,F10,N710,CGAGGCTG,S507,TACTCCTT
Configuration¶
experiment_name¶
Refers to the common Xavier Lab naming convention of <date_initials>. This will help set the Google bucket location of the input and output files for the experiment; genomics_xavier_bucket/<experiment_type>/<experiment_name>. As is customary, the bcl files that serve as the input to the pipeline must be in genomics_xavier_bucket/<experiment_type>/<experiment_name>/bcl and the fastq files will be written to genomics_xavier_bucket/<experiment_type>/<experiment_name>/fastq.
experiment_type¶
Denotes the type of experiment that was run. It must correspond to one of the directories listed here, as this parameter is used to set the location for output.
read_pairs_file¶
Location of the read_pairs.tsv file that will be generated as part of the pipeline.