diff --git a/.gitattributes b/.gitattributes index 5c94aa23bec94f86a2f5f6688a24ce1765c18f63..ecf1906c78c37404b2115cfff5d871cf6b22c978 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,2 +1,74 @@ **/dataset/** filter=lfs diff=lfs merge=lfs -text assays/rnaseq/dataset/** filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/10_H_GAGTGG_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/10_H_GAGTGG_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/10_H_GAGTGG_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/10_H_GAGTGG_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/11_H_ACTGAT_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/11_H_ACTGAT_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/11_H_ACTGAT_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/11_H_ACTGAT_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/12_H_ATTCCT_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/12_H_ATTCCT_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/12_H_ATTCCT_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/12_H_ATTCCT_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/13_S_M_CGATGT_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/13_S_M_CGATGT_L004_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/13_S_M_CGATGT_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/13_S_M_CGATGT_L004_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/14_S_M_TGACCA_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/14_S_M_TGACCA_L004_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/14_S_M_TGACCA_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/14_S_M_TGACCA_L004_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/15_S_M_ACAGTG_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/15_S_M_ACAGTG_L004_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/15_S_M_ACAGTG_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/15_S_M_ACAGTG_L004_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/16_S_H_GCCAAT_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/16_S_H_GCCAAT_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/17_S_H_CAGATC_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/17_S_H_CAGATC_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/18_S_H_CTTGTA_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/18_S_H_CTTGTA_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/19_M_H_AGTCAA_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/19_M_H_AGTCAA_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/1_C_ATCACG_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/1_C_ATCACG_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/1_C_ATCACG_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/1_C_ATCACG_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/20_M_H_AGTTCC_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/20_M_H_AGTTCC_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/21_M_H_ATGTCA_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/21_M_H_ATGTCA_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/22_S_M_H_CCGTCC_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/22_S_M_H_CCGTCC_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/23_S_M_H_GTCCGC_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/23_S_M_H_GTCCGC_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/24_S_M_H_GTGAAA_L004_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/24_S_M_H_GTGAAA_L004_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/2_C_TTAGGC_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/2_C_TTAGGC_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/2_C_TTAGGC_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/2_C_TTAGGC_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/3_C_ACTTGA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/3_C_ACTTGA_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/3_C_ACTTGA_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/3_C_ACTTGA_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/4_S_GATCAG_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/4_S_GATCAG_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/5_S_TAGCTT_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/5_S_TAGCTT_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/6_S_GGCTAC_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/6_S_GGCTAC_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/7_M_GTGGCC_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/7_M_GTGGCC_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/7_M_GTGGCC_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/7_M_GTGGCC_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/8_M_GTTTCG_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/8_M_GTTTCG_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/8_M_GTTTCG_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/8_M_GTTTCG_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/9_M_CGTACG_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/9_M_CGTACG_L002_R1_002.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/9_M_CGTACG_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text +/assays/rnaseq/dataset/9_M_CGTACG_L002_R2_002.fastq.gz filter=lfs diff=lfs merge=lfs -text diff --git a/assays/rnaseq/dataset/.gitkeep b/assays/rnaseq/dataset/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/rnaseq/protocols/samplesheet_run_0221.csv b/assays/rnaseq/protocols/samplesheet_run_0221.csv new file mode 100644 index 0000000000000000000000000000000000000000..d413ba5ccd5bb3d1bbe1fa90244028126e332ac1 --- /dev/null +++ b/assays/rnaseq/protocols/samplesheet_run_0221.csv @@ -0,0 +1,57 @@ +FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject +C6AYUACXX,1,US_MS7,human,ACTTGA,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,US_Mor9,human,TAGCTT,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,US_Mm6,human,CGTACG,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,DB_35_C3_MD,human,TTAGGC,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,DB_45_C3_MN,human,GATCAG,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,DB_65_CAM_MD,human,GTGGCC,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,DB_173_reC3_ED,human,GAGTGG,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,DB_201_reC3_EN,human,CGATGT,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,1,DB_77_CAM_MN,human,GCCAAT,Pool1,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,752_NGS_181214_0 +C6AYUACXX,2,1_C,human,ATCACG,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,2_C,human,TTAGGC,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,3_C,human,ACTTGA,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,4_S,human,GATCAG,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,5_S,human,TAGCTT,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,6_S,human,GGCTAC,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,7_M,human,GTGGCC,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,8_M,human,GTTTCG,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,9_M,human,CGTACG,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,10_H,human,GAGTGG,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,11_H,human,ACTGAT,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,2,12_H,human,ATTCCT,pool_green,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLiguleB2,human,AGTCAA,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.1,Wachtmeister,592_NGS_300914_0 +C6AYUACXX,3,PmaxLiguleM2,human,GTCCGC,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLiguleT2,human,GTGAAA,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf1_2,human,CGATGT,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf2_2,human,TGACCA,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf3_2,human,ATTCCT,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf4_2,human,ACAGTG,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,DclaLiguleM2,human,CTTGTA,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf6_2,human,AGTTCC,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf7_2,human,GCCAAT,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,3,PmaxLeaf8_2,human,CCGTCC,pool_4_red,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,13_S_M,human,CGATGT,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,14_S_M,human,TGACCA,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,15_S_M,human,ACAGTG,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,16_S_H,human,GCCAAT,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,17_S_H,human,CAGATC,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,18_S_H,human,CTTGTA,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,19_M_H,human,AGTCAA,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,20_M_H,human,AGTTCC,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,21_M_H,human,ATGTCA,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,22_S_M_H,human,CCGTCC,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,23_S_M_H,human,GTCCGC,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,4,24_S_M_H,human,GTGAAA,pool_8,N,PE_Amp_Lin_Block_tubeStripHybv8.0,Wachtmeister,593_NGS_300914_0 +C6AYUACXX,5,M62474,human,AGGCAG,RSS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool4 +C6AYUACXX,5,M62475,human,TCCTGA,RSS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool4 +C6AYUACXX,5,M62476,human,TAGGCA,RSS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool4 +C6AYUACXX,6,M62477,human,GTAGAG,RSS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool5 +C6AYUACXX,6,M36871,human,CTCTCT,AS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool5 +C6AYUACXX,6,M38729,human,CAGAGA,AS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool5 +C6AYUACXX,7,M59106,human,TAAGGC,BWS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool6 +C6AYUACXX,7,M59107,human,CGTACT,BWS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool6 +C6AYUACXX,7,M59105,human,TCCTGA,BWS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool6 +C6AYUACXX,8,M61284,human,GTAGAG,BWS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool7 +C6AYUACXX,8,M61285,human,CTCTCT,BWS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool7 +C6AYUACXX,8,M61286,human,CAGAGA,BWS,N,PE_Amp_Lin_Block_tubeStripHybv8.0,CH,Buiting_Pool7