@HD VN:1.4 SO:coordinate @RG ID:1#260 PL:ILLUMINA PU:170413_HS40_22287_A_HGJ5HADXY_1#260 LB:18966105 DS:EGAS00001002325: We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. DT:2017-04-13T00:00:00+0100 SM:EGAN00001514551 PG:BamIndexDecoder CN:SC @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:2.2.68 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.18.66.3 @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.17 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities BASECALLS_DIR=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001514560,EGAN00001514561,EGAN00001514562,EGAN00001514563,EGAN00001514564,EGAN00001514565,EGAN00001514566,EGAN00001514567,EGAN00001514568,EGAN00001514569,EGAN00001514570,EGAN00001514571,EGAN00001514572,EGAN00001514573,EGAN00001514574,EGAN00001514575,EGAN00001514576,EGAN00001514577,EGAN00001514578,EGAN00001514579,EGAN00001514580,EGAN00001514581,EGAN00001514582,EGAN00001514583,EGAN00001514584,EGAN00001514585,EGAN00001514600,EGAN00001514601,EGAN00001514602,EGAN00001514603,EGAN00001514604,EGAN00001514605,EGAN00001514606,EGAN00001514607,EGAN00001514608,EGAN00001514609,EGAN00001514610,EGAN00001514586,EGAN00001514587,EGAN00001514588,EGAN00001514589,EGAN00001514590,EGAN00001514591,EGAN00001514592,EGAN00001514593,EGAN00001514594,EGAN00001514595,EGAN00001514596,EGAN00001514597,EGAN00001514598,EGAN00001514599,EGAN00001514611,EGAN00001514612,EGAN00001514613,EGAN00001514614,EGAN00001514615,EGAN00001514616,EGAN00001514617,EGAN00001514618,EGAN00001514619,EGAN00001514620,EGAN00001514621,EGAN00001514622,EGAN00001514623,EGAN00001514624,EGAN00001514625,EGAN00001514626,EGAN00001514627,EGAN00001514628,EGAN00001514629,EGAN00001514630,EGAN00001514631,EGAN00001514632,EGAN00001514633,EGAN00001514634,EGAN00001514635,EGAN00001514636,EGAN00001514637,EGAN00001514638,EGAN00001514639,EGAN00001514640,EGAN00001514641,EGAN00001514642,EGAN00001514643,EGAN00001514644,EGAN00001514645,EGAN00001514646,EGAN00001514647,EGAN00001514648,EGAN00001514649,EGAN00001514650,EGAN00001514651,EGAN00001514652,EGAN00001514653,EGAN00001514654,EGAN00001514655,EGAN00001514656,EGAN00001514657,EGAN00001514658,EGAN00001514659,EGAN00001514660,EGAN00001514661,EGAN00001514662,EGAN00001514663,EGAN00001514664,EGAN00001514665,EGAN00001514470,EGAN00001514471,EGAN00001514472,EGAN00001514473,EGAN00001514474,EGAN00001514475,EGAN00001514476,EGAN00001514477,EGAN00001514478,EGAN00001514479,EGAN00001514480,EGAN00001514481,EGAN00001514666,EGAN00001514667,EGAN00001514668,EGAN00001514669,EGAN00001514670,EGAN00001514671,EGAN00001514672,EGAN00001514673,EGAN00001514674,EGAN00001514675,EGAN00001514676,EGAN00001514677,EGAN00001514482,EGAN00001514483,EGAN00001514484,EGAN00001514485,EGAN00001514486,EGAN00001514487,EGAN00001514488,EGAN00001514489,EGAN00001514490,EGAN00001514491,EGAN00001514492,EGAN00001514493,EGAN00001514678,EGAN00001514679,EGAN00001514680,EGAN00001514681,EGAN00001514682,EGAN00001514683,EGAN00001514684,EGAN00001514685,EGAN00001514686,EGAN00001514687,EGAN00001514688,EGAN00001514689,EGAN00001514494,EGAN00001514495,EGAN00001514496,EGAN00001514497,EGAN00001514498,EGAN00001514499,EGAN00001514500,EGAN00001514501,EGAN00001514502,EGAN00001514503,EGAN00001514504,EGAN00001514505,EGAN00001514690,EGAN00001514691,EGAN00001514692,EGAN00001514693,EGAN00001514694,EGAN00001514695,EGAN00001514696,EGAN00001514697,EGAN00001514698,EGAN00001514699,EGAN00001514700,EGAN00001514701,EGAN00001514506,EGAN00001514507,EGAN00001514508,EGAN00001514509,EGAN00001514510,EGAN00001514511,EGAN00001514512,EGAN00001514513,EGAN00001514514,EGAN00001514515,EGAN00001514516,EGAN00001514702,EGAN00001514703,EGAN00001514704,EGAN00001514705,EGAN00001514706,EGAN00001514707,EGAN00001514708,EGAN00001514709,EGAN00001514710,EGAN00001514711,EGAN00001514712,EGAN00001514713,EGAN00001514517,EGAN00001514518,EGAN00001514519,EGAN00001514520,EGAN00001514521,EGAN00001514522,EGAN00001514523,EGAN00001514524,EGAN00001514525,EGAN00001514526,EGAN00001514527,EGAN00001514714,EGAN00001514715,EGAN00001514716,EGAN00001514717,EGAN00001514718,EGAN00001514719,EGAN00001514720,EGAN00001514721,EGAN00001514722,EGAN00001514723,EGAN00001514724,EGAN00001514725,EGAN00001514528,EGAN00001514529,EGAN00001514530,EGAN00001514531,EGAN00001514532,EGAN00001514533,EGAN00001514534,EGAN00001514535,EGAN00001514536,EGAN00001514537,EGAN00001514538,EGAN00001514539,EGAN00001514726,EGAN00001514727,EGAN00001514728,EGAN00001514729,EGAN00001514730,EGAN00001514731,EGAN00001514732,EGAN00001514733,EGAN00001514734,EGAN00001514735,EGAN00001514736,EGAN00001514737,EGAN00001514540,EGAN00001514541,EGAN00001514542,EGAN00001514543,EGAN00001514544,EGAN00001514545,EGAN00001514546,EGAN00001514547,EGAN00001514548,EGAN00001514549,EGAN00001514550,EGAN00001514551,EGAN00001514738,EGAN00001514739,EGAN00001514740,EGAN00001514741,EGAN00001514742,EGAN00001514743,EGAN00001514744,EGAN00001514745,EGAN00001514746,EGAN00001514747,EGAN00001514552,EGAN00001514553,EGAN00001514554,EGAN00001514555,EGAN00001514556,EGAN00001514557,EGAN00001514558,EGAN00001514559 STUDY_NAME=EGAS00001002325: We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. PLATFORM_UNIT=170413_HS40_22287_A_HGJ5HADXY_1 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:2.0.8 CL:bamadapterfind level=0 @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.17 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/metadata_cache_22287/lane_1.taglist METRICS_FILE=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/22287_1.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.22-dirty CL:/nfs/gs01/software/pkg/pb_calibration/10.22/bin/spatial_filter -c -F pb_align_22287_1.bam.filter -t /nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/qc/tileviz/22287_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_22287_1.bam ; /nfs/gs01/software/pkg/pb_calibration/10.22/bin/spatial_filter -a -f -u -F pb_align_22287_1.bam.filter - @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx @PG ID:BamMerger PN:BamMerger PP:bwa DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.17 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_22287_1.bam INPUT=/dev/stdin OUTPUT=22287_1.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.17 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/22287_1.bam OUTPUT_PREFIX=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1 OUTPUT_COMMON_RG_HEAD_TO_TRIM=1 VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bwa_aln PN:bwa PP:SplitBamByReadGroup VN:0.5.10-tpx CL:/nfs/gs01/software/pkg/bwa/0.5.10-mt_fixes.2/bwa aln -q 15 -t 7 /nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa -b1 /nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1#260.bam > /tmp/RENnJEXXtt/1.sai @PG ID:bwa_aln_1 PN:bwa PP:bwa_aln VN:0.5.10-tpx CL:/nfs/gs01/software/pkg/bwa/0.5.10-mt_fixes.2/bwa aln -q 15 -t 7 /nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa -b2 /nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1#260.bam > /tmp/RENnJEXXtt/2.sai @PG ID:bwa_sam PN:bwa PP:bwa_aln_1 VN:0.5.10-tpx CL:/nfs/gs01/software/pkg/bwa/0.5.10-mt_fixes.2/bwa sampe -t 6 /nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa /tmp/RENnJEXXtt/1.sai /tmp/RENnJEXXtt/2.sai /nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1#260.bam /nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1#260.bam @PG ID:Picard_SamFormatConverter PN:SamFormatConverter PP:bwa_sam VN:1.72(1230) CL:/usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java -Xmx1000m -jar /nfs/gs01/software/pkg/picard/1.72/SamFormatConverter.jar VALIDATION_STRINGENCY=SILENT INPUT=/dev/stdin OUTPUT=/dev/stdout COMPRESSION_LEVEL=0 @PG ID:samtools_fixmate PN:samtools PP:Picard_SamFormatConverter VN:0.1.18 (r982:295) CL:/nfs/gs01/software/pkg/samtools/0.1.18/samtools fixmate - - @PG ID:BamMerger_1 PN:BamMerger PP:samtools_fixmate VN:V1.17 DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=/dev/stdin ALIGNMENT_PROGRAM_ID=NULL KEEP_ALL_PG=true INPUT=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1#260.bam OUTPUT=/tmp/RENnJEXXtt/output_fifo.bam KEEP_EXTRA_UNMAPPED_READS=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true REPLACE_ALIGNED_BASE_QUALITY=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:AlignmentFilter PN:AlignmentFilter PP:BamMerger_1 DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.17 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/lane1/22287_1#260.bam, /tmp/RENnJEXXtt/output_fifo.bam] OUTPUT_ALIGNMENT=[/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/lane1/22287_1#260_phix.bam, /nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/lane1/22287_1#260.bam] METRICS_FILE=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/lane1/22287_1#260.bam_alignment_filter_metrics.json VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bamsort PN:bamsort CL:/nfs/gs01/software/pkg/biobambam/2.0.8/bin/bamsort tmpfile=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/lane1/270CEV9l_Y/ PP:AlignmentFilter VN:2.0.8 @PG ID:bammarkduplicates2 PN:bammarkduplicates2 CL:/nfs/gs01/software/pkg/biobambam/2.0.8/bin/bammarkduplicates2 I=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/lane1/270CEV9l_Y/sorted.bam O=/dev/stdout tmpfile=/nfs/gs02/IL_seq_data/analysis/170413_HS40_22287_A_HGJ5HADXY/Data/Intensities/BAM_basecalls_20170414-082411/no_cal/archive/lane1/270CEV9l_Y/ M=/tmp/W9liHThQiU PP:bamsort VN:2.0.8 @PG ID:scramble PN:scramble PP:bammarkduplicates2 VN:1.13.10 CL:/nfs/gs01/software/pkg/staden_io_lib/1.13.10/bin/scramble -I bam -O cram -r /nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:1 LN:249250621 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human @SQ SN:2 LN:243199373 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a0d9851da00400dec1098a9255ac712e SP:Human @SQ SN:3 LN:198022430 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Human @SQ SN:4 LN:191154276 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:23dccd106897542ad87d2765d28a19a1 SP:Human @SQ SN:5 LN:180915260 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0740173db9ffd264d728f32784845cd7 SP:Human @SQ SN:6 LN:171115067 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Human @SQ SN:7 LN:159138663 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:618366e953d6aaad97dbe4777c29375e SP:Human @SQ SN:8 LN:146364022 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:96f514a9929e410c6651697bded59aec SP:Human @SQ SN:9 LN:141213431 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:3e273117f15e0a400f01055d9f393768 SP:Human @SQ SN:10 LN:135534747 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:988c28e000e84c26d552359af1ea2e1d SP:Human @SQ SN:11 LN:135006516 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Human @SQ SN:12 LN:133851895 UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:51851ac0e1a115847ad36449b0015864 SP:Human @SQ SN:13 LN:115169878 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