SampleSheets - HackMD

# SampleSheets ### Novaseq Som det ser ut just nu: ``` [Header],,,,,,,,,, IEMFileVersion,5,,,,,,,,, Investigator Name,SH,,,,,,,,, Experiment Name,WGS_Prep54_Pool54_201127_SH,,,,,,,,, Date,2020-11-27,,,,,,,,, Workflow,GenerateFASTQ,,,,,,,,, Application,NovaSeq FASTQ Only,,,,,,,,, Instrument Type,NovaSeq,,,,,,,,, Assay,TruSeq DNA PCR-Free,,,,,,,,, Chemistry,Amplicon,,,,,,,,, ,,,,,,,,,, [Reads],,,,,,,,,, 151,,,,,,,,,, 151,,,,,,,,,, ,,,,,,,,,, [Settings],,,,,,,,,, Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,, AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,, ,,,,,,,,,, [Data],,,,,,,,,, Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_Plate_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description DNA70860,DNA70860_201127_AHGGVGDSXY,,,A01,UDI0001,CCGCGGTT,UDI0001,AGCGCTAG,KG,CGG_M_00_i_70860_ DNA71107,DNA71107_201127_AHGGVGDSXY,,,B01,UDI0002,TTATAACC,UDI0002,GATATCGA,KG,CGG_M_00_far_70860_ DNA71108,DNA71108_201127_AHGGVGDSXY,,,C01,UDI0003,GGACTTGG,UDI0003,CGCAGACG,KG,CGG_F_00_mor_70860_ ``` #### Beslut: Fortsätter som är just nu ### Nextseq Som det ser ut nu: ``` [Header],,,,,,,,,, IEMFileVersion,5,,,,,,,,, Investigator Name,AS-GS,,,,,,,,, Experiment Name,Twist-hematolg-panel,,,,,,,,, Date,8/20/2020,,,,,,,,, Workflow,GenerateFASTQ,,,,,,,,, Application,NextSeq FASTQ Only,,,,,,,,, Instrument Type,NextSeq/MiniSeq,,,,,,,,, Assay,TruSeq Nano DNA,,,,,,,,, Index Adapters,TruSeq DNA CD Indexes (96 Indexes),,,,,,,,, Chemistry,Amplicon,,,,,,,,, ,,,,,,,,,, [Reads],,,,,,,,,, 151,,,,,,,,,, 151,,,,,,,,,, ,,,,,,,,,, [Settings],,,,,,,,,, Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,, AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,, Read1UMILength,3,,,,,,,,, Read2UMILength,3,,,,,,,,, Read1StartFromCycle,6,,,,,,,,, Read2StartFromCycle,6,,,,,,,,, ,,,,,,,,,, [Data],,,,,,,,,, Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_Plate_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description T1,T1,,,A04,i7-1,CCTTGATC,i5-1,GATGGAGT,kk,gms-myeloid_tp53 T2,T2,,,B04,i7-2,GTCGAAGA,i5-2,CCACATTG,kk,gms-myeloid_all T3,T3,,,C04,i7-3,ACCACGAT,i5-3,GTCTGCAA,kk,gms-myeloid_all T4,T4,,,D04,i7-4,GATTACCG,i5-4,TTGGACTG,kk,gms-myeloid_all T5,T5,,,E04,i7-5,GCACAACT,i5-5,CTGAACGT,kk,gms-myeloid_tp53 T6,T6,,,F04,i7-6,GCGTCATT,i5-6,CAGACGTT,kk,gms-myeloid_all T7,T7,,,G04,i7-7,ATCCGGTA,i5-7,GACCGATA,kk,gms-myeloid_all HD829,HD829,,,H04,i7-8,CGTTGCAA,i5-8,ATAGAGCG,kk,gms-myeloid_all N1,N1,,,A05,i7-9,GTGAAGTG,i5-9,GAGCAATC,kk,gms-myeloid_all N2,N2,,,B05,i7-10,CATGGCTA,i5-10,CACACATC,kk,gms-myeloid_all N3,N3,,,C05,i7-11,ATGCCTGT,i5-11,AGATTGCG,kk,gms-myeloid_all N4,N4,,,D05,i7-12,CAACACCT,i5-12,AGCTACCA,kk,gms-myeloid_all N5,N5,,,E05,i7-13,TGTGACTG,i5-13,AGCCTATC,kk,gms-myeloid_all N6,N6,,,F05,i7-14,GTCATCGA,i5-14,GATCCACT,kk,gms-myeloid_all N7,N7,,,G05,i715,AGCACTTC,i5-15,ACGTCCAA,kk,gms-myeloid_all ``` #### Beslut * Sample_Project=KK får endast användas av de prover som ska in i SLIMS * I description fältet ska "gms_myeloid_all" eller "gms_myelooid_tp53" anges. Om det är tomt blir det "all" som default. * Giti och Anna Staffas behöver den informationen * Använd unika namn för Sample_ID/Sample_Name ### Miseq Som det ser ut nu: ``` [Header] IEMFileVersion,4 Investigator Name,GA Experiment Name,myeloidpanel Date,2020-11-25 Workflow,Custom Amplicon Application,TruSeq Amplicon Assay,TruSeq Amplicon Description,201125pool Chemistry,Amplicon [Manifests] A,TruSight-Myeloid-Manifest.txt [Reads] 201 201 [Settings] VariantCaller,Somatic VariantFilterQualityCutoff,30 outputgenomevcf,TRUE [Data] Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Manifest,GenomeFolder,Sample_Project,Description 620200890,,,,A707,CCCAACCT,A501,TGAACCTT,A,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta,, 620200907,,,,A707,CCCAACCT,A502,TGCTAAGT,A,Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta,, ``` NPM1: ``` [Header],,,,,,,,, IEMFileVersion,4,,,,,,,, Investigator Name,GS,,,,,,,, Experiment Name,UDS_NPM1_BM_glas_flowcell39_4nM,,,,,,,, Date,10/6/2020,,,,,,,, Workflow,GenerateFASTQ,,,,,,,, Application,FASTQ Only,,,,,,,, Assay,TruSeq HT,,,,,,,, Description,NPM1,,,,,,,, Chemistry,Amplicon,,,,,,,, ,,,,,,,,, [Reads],,,,,,,,, 151,,,,,,,,, 151,,,,,,,,, ,,,,,,,,, [Settings],,,,,,,,, ,,,,,,,,, [Data],,,,,,,,, Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description UDS_NPM1_55773034_,UDS_NPM1_55773034_,,,A701,ATCACGAC,A501,TGAACCTT,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NOPHO_Normal_TSPAN15,UDS_NOPHO_Normal_TSPAN15,,,A702,ACAGTGGT,A502,TGCTAAGT,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NPM1_55773055,UDS_NPM1_55773055,,,A703,CAGATCCA,A503,TGTTCTCT,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NPM1_55773079,UDS_NPM1_55773079,,,A704,ACAAACGG,A504,TAAGACAC,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NPM1_55773080,UDS_NPM1_55773080,,,A705,ACCCAGCA,A505,CTAATCGA,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NPM1_BM_glas_25016028,UDS_NPM1_BM_glas_25016028,,,A708,CACCACAC,A506,CTAGAACA,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NPM1_BM_glas_25016052,UDS_NPM1_BM_glas_25016052,,,A709,GAAACCCA,A507,TAAGTTCC,UDS_NPM1_BM_glas_F39,MRD_AML UDS_NPM1_BM_glas_25160464wt,UDS_NPM1_BM_glas_25160464wt,,,A710,TGTGACCA,A508,TAGACCTA,UDS_NPM1_BM_glas_F39,MRD_AML ``` #### Beslut: Vi fortsätter som vanligt

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