From 7ee1f3a1f570e438fdad042e74a29bbdb8eabd5b Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 27 Feb 2024 15:17:00 +0000 Subject: [PATCH] Allow for legitimate duplicate libraries. When considering aggregation of lims objects by library, do not consider the same library with different tag index in the same lane as a error. Chromium single cell ATAC libraries have 4x copies of each sample each with a different tag. --- Changes | 7 +++ MANIFEST | 1 + lib/st/api/lims.pm | 38 +++++++++--- t/40-st-lims-merge.t | 38 +++++++++--- .../samplesheet_singlecell_48460.csv | 60 +++++++++++++++++++ 5 files changed, 129 insertions(+), 15 deletions(-) create mode 100644 t/data/samplesheet/samplesheet_singlecell_48460.csv diff --git a/Changes b/Changes index 8327a461..28e268b9 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,12 @@ LIST OF CHANGES + +release 100.0.1 + - For aggregation of lims objects by library in st::api::lims, do not + consider the same library with different tag index in the same lane + as a error. Chromium single cell ATAC libraries have four copies of + each sample, each with a different tag. + release 100.0.0 - To help monitor shadow run folders, include the run folder path into the logging messages in the staging monitor classes code. diff --git a/MANIFEST b/MANIFEST index a6581893..9cdfc37c 100644 --- a/MANIFEST +++ b/MANIFEST @@ -669,6 +669,7 @@ t/data/samplesheet/samplesheet_7753.csv t/data/samplesheet/samplesheet_27483.csv t/data/samplesheet/samplesheet_33990.csv t/data/samplesheet/samplesheet_47995.csv +t/data/samplesheet/samplesheet_singlecell_48460.csv t/data/samplesheet/4pool4libs_extended.csv t/data/samplesheet/6946_extended.csv t/data/samplesheet/7007_extended.csv diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 1330249f..12c77247 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -873,7 +873,7 @@ sub aggregate_libraries { if ($obj->is_control()) { push @singles, $obj; } else { - push @{$lims_objects_by_library->{$obj->library_id}}, $obj; + push @{$lims_objects_by_library->{_hash_key4lib_aggregation($obj)}}, $obj; } } @@ -885,13 +885,27 @@ sub aggregate_libraries { delete $init->{position}; delete $init->{id_run}; + my @non_control_singles = map { $_->[0] } + grep { scalar @{$_} == 1 } + values %{$lims_objects_by_library}; + push @singles, @non_control_singles; + + my %lanes_with_singles = map { $_->position => 1 } + @non_control_singles; + my $merges = {}; my $lane_set_delim = q[,]; - foreach my $library_id (keys %{$lims_objects_by_library}) { - my @lib_lims = @{$lims_objects_by_library->{$library_id}}; - if (@lib_lims == 1) { - push @singles, @lib_lims; - } else { + foreach my $hashing_key (keys %{$lims_objects_by_library}) { + my @lib_lims = @{$lims_objects_by_library->{$hashing_key}}; + if (@lib_lims > 1) { + + # If some libraries from the lane cannot be merged, other libraries + # will not be merged either. This might change in future. + if (any { exists $lanes_with_singles{$_->position} } @lib_lims) { + push @singles, @lib_lims; + next; + } + _check_merge_correctness(\@lib_lims); my $lane_set = join $lane_set_delim, sort { $a <=> $b } map { $_->position } @lib_lims; @@ -951,14 +965,22 @@ sub aggregate_libraries { return $all_lims_objects; } +sub _hash_key4lib_aggregation { + my $lims_obj = shift; + my $key = $lims_obj->library_id; + if (defined $lims_obj->tag_index) { + $key .= q[:] . $lims_obj->tag_index; + } + return $key; +} + sub _check_merge_correctness { my $lib_lims = shift; my @lanes = uniq map {$_->position} @{$lib_lims}; - if (@lanes != @{$lib_lims}) { + if (@lanes != @{$lib_lims}) { # An unlikely mistake somewhere upstream. croak 'Intra-lane merge is detected'; } _check_value_is_unique('study_id', 'studies', $lib_lims); - _check_value_is_unique('tag_index', 'tag indexes', $lib_lims); return; } diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index 605f1131..085c0efc 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 9; +use Test::More tests => 10; use Test::Exception; use List::MoreUtils qw/all none/; use File::Slurp; @@ -130,7 +130,7 @@ subtest 'Create tag zero object' => sub { }; subtest 'Error conditions in aggregation by library' => sub { - plan tests => 4; + plan tests => 3; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; @@ -160,19 +160,43 @@ subtest 'Error conditions in aggregation by library' => sub { throws_ok { st::api::lims->aggregate_libraries(\@lane_lims) } qr/Multiple studies in a potential merge by library/, 'can only merge libraries that belong to the same study'; +}; + +subtest 'Allow duplicate libraries with different tag indexes' => sub { + plan tests => 6; - $content = read_file($ss_47995_path); + # Real life example: Chromium single cell ATAC libraries have 4 copies + # of each sample in a lane, each with a different tag. + # This should not cause an error. + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/samplesheet_singlecell_48460.csv'; + my @lane_lims = st::api::lims->new(id_run => 48460)->children; + my $lims; + lives_ok { $lims = st::api::lims->aggregate_libraries(\@lane_lims) } + 'no error since grouping by library ID and tag index'; + is (scalar @{$lims->{merges}}, 28, '28 merged libraries'); + is (scalar @{$lims->{singles}}, 2, '2 single libraries'); + + # Testing below that if one library in a potentially meargeable lane + # is a singleton, the whole lane is excluded from the merge. + + my $content = read_file('t/data/samplesheet/samplesheet_47995.csv'); # Make library id of tag 1 lane 1 the same as for tag 2 lane 3. $content =~ s/1,65934716,/1,69723083,/; # Change study id for all tags of lane 3 to be the same as in lane 1. $content =~ s/,6050,/,6751,/g; - $file_path = join q[/], $tmp_dir, 'samplesheet_multi_tag.csv'; + my $file_path = join q[/], $tmp_dir, 'samplesheet_multi_tag.csv'; write_file($file_path, $content); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $file_path; @lane_lims = st::api::lims->new(id_run => 47995)->children; - throws_ok { st::api::lims->aggregate_libraries(\@lane_lims) } - qr/Multiple tag indexes in a potential merge by library/, - 'can only merge libraries with teh same tag index'; + lives_ok { $lims = st::api::lims->aggregate_libraries(\@lane_lims) } + 'no error since grouping by library ID and tag index'; + my @unexpected = grep { $_ =~ / ^1: / } + map { $_->rpt_list } @{$lims->{merges}}; + is (scalar @unexpected, 0, 'lane 1 is not in merged entities'); + # 8 controls + 17 in lanes 1 and 2 each + is (scalar @{$lims->{singles}}, 42, '42 single libraries'); }; subtest 'Aggregation by library for a NovaSeq standard flowcell' => sub { diff --git a/t/data/samplesheet/samplesheet_singlecell_48460.csv b/t/data/samplesheet/samplesheet_singlecell_48460.csv new file mode 100644 index 00000000..734b53b7 --- /dev/null +++ b/t/data/samplesheet/samplesheet_singlecell_48460.csv @@ -0,0 +1,60 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,purpose,qc_state,required_insert_size_range,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_id,sample_is_control,sample_public_name,sample_reference_genome,spiked_phix_tag_index,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_id,study_reference_genome,study_separate_y_chromosome_data,tag_index, +1,70854676,EGAN00004484592,,AATCACTA,,,Chromium single cell ATAC,AATCACTA,,,0,0,71209965,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,1, +1,70854676,EGAN00004484592,,CCGAGAAC,,,Chromium single cell ATAC,CCGAGAAC,,,0,0,71209965,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,2, +1,70854676,EGAN00004484592,,GTAGTGCG,,,Chromium single cell ATAC,GTAGTGCG,,,0,0,71209965,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,3, +1,70854676,EGAN00004484592,,TGCTCTGT,,,Chromium single cell ATAC,TGCTCTGT,,,0,0,71209965,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B 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(GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,7, +1,70854677,EGAN00004484591,,TGTGATGC,,,Chromium single cell ATAC,TGTGATGC,,,0,0,71209965,0,70854677,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566293,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,8, +1,70854579,EGAN00004484588,,ACGTTACA,,,Chromium single cell ATAC,ACGTTACA,,,0,0,71209965,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,9, +1,70854579,EGAN00004484588,,CGTAGGTT,,,Chromium single cell ATAC,CGTAGGTT,,,0,0,71209965,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,10, +1,70854579,EGAN00004484588,,GACGACGG,,,Chromium single cell ATAC,GACGACGG,,,0,0,71209965,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,11, +1,70854579,EGAN00004484588,,TTACCTAC,,,Chromium single cell ATAC,TTACCTAC,,,0,0,71209965,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,12, +1,70854580,EGAN00004484589,,ACTTCACT,,,Chromium single cell ATAC,ACTTCACT,,,0,0,71209965,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,13, +1,70854580,EGAN00004484589,,CGAAGTTG,,,Chromium single cell ATAC,CGAAGTTG,,,0,0,71209965,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,14, +1,70854580,EGAN00004484589,,GAGCACGC,,,Chromium single cell ATAC,GAGCACGC,,,0,0,71209965,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,15, +1,70854580,EGAN00004484589,,TTCGTGAA,,,Chromium single cell ATAC,TTCGTGAA,,,0,0,71209965,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,16, +1,70854675,EGAN00004484590,,AACAAGTC,,,Chromium single cell ATAC,AACAAGTC,,,0,0,71209965,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,17, +1,70854675,EGAN00004484590,,CGGCTCCA,,,Chromium single cell ATAC,CGGCTCCA,,,0,0,71209965,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,18, +1,70854675,EGAN00004484590,,GTATGTAT,,,Chromium single cell ATAC,GTATGTAT,,,0,0,71209965,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,19, +1,70854675,EGAN00004484590,,TCTGCAGG,,,Chromium single cell ATAC,TCTGCAGG,,,0,0,71209965,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,20, +1,70854771,EGAN00004484593,,AGTCTGTA,,,Chromium single cell ATAC,AGTCTGTA,,,0,0,71209965,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,21, +1,70854771,EGAN00004484593,,CAGAATAG,,,Chromium single cell ATAC,CAGAATAG,,,0,0,71209965,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,22, +1,70854771,EGAN00004484593,,GCCTCCGT,,,Chromium single cell ATAC,GCCTCCGT,,,0,0,71209965,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,23, +1,70854771,EGAN00004484593,,TTAGGACC,,,Chromium single cell ATAC,TTAGGACC,,,0,0,71209965,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,24, +1,70854772,EGAN00004484594,,ATGTCCAG,,,Chromium single cell ATAC,ATGTCCAG,,,0,0,71209965,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,25, +1,70854772,EGAN00004484594,,CGACGTCA,,,Chromium single cell ATAC,CGACGTCA,,,0,0,71209965,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,26, +1,70854772,EGAN00004484594,,GCTATAGC,,,Chromium single cell ATAC,GCTATAGC,,,0,0,71209965,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,27, +1,70854772,EGAN00004484594,,TACGAGTT,,,Chromium single cell ATAC,TACGAGTT,,,0,0,71209965,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,28, +1,51702667,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,1,0,71209965,0,51702667,,10847,,standard,1,,,,0,,,1255141,,,PhiX (Sanger-SNPs),888,1,0,0,198, ,0,888, +2,70854676,EGAN00004484592,,AATCACTA,,,Chromium single cell ATAC,AATCACTA,,,0,0,71209966,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,1, +2,70854676,EGAN00004484592,,CCGAGAAC,,,Chromium single cell ATAC,CCGAGAAC,,,0,0,71209966,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,2, +2,70854676,EGAN00004484592,,GTAGTGCG,,,Chromium single cell ATAC,GTAGTGCG,,,0,0,71209966,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,3, +2,70854676,EGAN00004484592,,TGCTCTGT,,,Chromium single cell ATAC,TGCTCTGT,,,0,0,71209966,0,70854676,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566292,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,4, +2,70854677,EGAN00004484591,,ACATTCCG,,,Chromium single cell ATAC,ACATTCCG,,,0,0,71209966,0,70854677,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566293,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,5, +2,70854677,EGAN00004484591,,CTGCGGTA,,,Chromium single cell ATAC,CTGCGGTA,,,0,0,71209966,0,70854677,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566293,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,6, +2,70854677,EGAN00004484591,,GACACAAT,,,Chromium single cell ATAC,GACACAAT,,,0,0,71209966,0,70854677,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566293,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,7, +2,70854677,EGAN00004484591,,TGTGATGC,,,Chromium single cell ATAC,TGTGATGC,,,0,0,71209966,0,70854677,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566293,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,8, +2,70854579,EGAN00004484588,,ACGTTACA,,,Chromium single cell ATAC,ACGTTACA,,,0,0,71209966,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,9, +2,70854579,EGAN00004484588,,CGTAGGTT,,,Chromium single cell ATAC,CGTAGGTT,,,0,0,71209966,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,10, +2,70854579,EGAN00004484588,,GACGACGG,,,Chromium single cell ATAC,GACGACGG,,,0,0,71209966,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,11, +2,70854579,EGAN00004484588,,TTACCTAC,,,Chromium single cell ATAC,TTACCTAC,,,0,0,71209966,0,70854579,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566289,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,12, +2,70854580,EGAN00004484589,,ACTTCACT,,,Chromium single cell ATAC,ACTTCACT,,,0,0,71209966,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,13, +2,70854580,EGAN00004484589,,CGAAGTTG,,,Chromium single cell ATAC,CGAAGTTG,,,0,0,71209966,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,14, +2,70854580,EGAN00004484589,,GAGCACGC,,,Chromium single cell ATAC,GAGCACGC,,,0,0,71209966,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,15, +2,70854580,EGAN00004484589,,TTCGTGAA,,,Chromium single cell ATAC,TTCGTGAA,,,0,0,71209966,0,70854580,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566290,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,7336,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,16, +2,70854675,EGAN00004484590,,AACAAGTC,,,Chromium single cell ATAC,AACAAGTC,,,0,0,71209966,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,17, +2,70854675,EGAN00004484590,,CGGCTCCA,,,Chromium single cell ATAC,CGGCTCCA,,,0,0,71209966,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,18, +2,70854675,EGAN00004484590,,GTATGTAT,,,Chromium single cell ATAC,GTATGTAT,,,0,0,71209966,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,19, +2,70854675,EGAN00004484590,,TCTGCAGG,,,Chromium single cell ATAC,TCTGCAGG,,,0,0,71209966,0,70854675,,9606,S10501,standard,1,from:100 to:1000,,human,0,,,9566291,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6768,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,20, +2,70854771,EGAN00004484593,,AGTCTGTA,,,Chromium single cell ATAC,AGTCTGTA,,,0,0,71209966,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,21, +2,70854771,EGAN00004484593,,CAGAATAG,,,Chromium single cell ATAC,CAGAATAG,,,0,0,71209966,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,22, +2,70854771,EGAN00004484593,,GCCTCCGT,,,Chromium single cell ATAC,GCCTCCGT,,,0,0,71209966,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,23, +2,70854771,EGAN00004484593,,TTAGGACC,,,Chromium single cell ATAC,TTAGGACC,,,0,0,71209966,0,70854771,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566294,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,24, +2,70854772,EGAN00004484594,,ATGTCCAG,,,Chromium single cell ATAC,ATGTCCAG,,,0,0,71209966,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,25, +2,70854772,EGAN00004484594,,CGACGTCA,,,Chromium single cell ATAC,CGACGTCA,,,0,0,71209966,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,26, +2,70854772,EGAN00004484594,,GCTATAGC,,,Chromium single cell ATAC,GCTATAGC,,,0,0,71209966,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,27, +2,70854772,EGAN00004484594,,TACGAGTT,,,Chromium single cell ATAC,TACGAGTT,,,0,0,71209966,0,70854772,,9606,S4674,standard,1,from:100 to:1000,,human,0,,,9566295,,,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,888,1,0,0,6291,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,0,28, +2,51702667,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,1,0,71209966,0,51702667,,10847,,standard,1,,,,0,,,1255141,,,PhiX (Sanger-SNPs),888,1,0,0,198, ,0,888, \ No newline at end of file