From 01681ce0df0b5f4fedd8e07801d937fc027bc084 Mon Sep 17 00:00:00 2001 From: massonix Date: Tue, 5 Dec 2023 00:24:06 +0100 Subject: [PATCH] CR multiome 2 --- .../hagf3y16_sldip2ou/hagf3y16_sldip2ou.cmd | 18 + .../hagf3y16_sldip2ou/outs/summary.csv | 2 + .../hagf3y16_sldip2ou/outs/web_summary.html | 324 ++++++++++++++++++ .../jobs/hagf3y16_sldip2ou/libraries.csv | 5 + .../k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq.cmd | 17 + .../k8s4gkxa_phcaecsq/outs/summary.csv | 2 + .../k8s4gkxa_phcaecsq/outs/web_summary.html | 324 ++++++++++++++++++ .../jobs/k8s4gkxa_phcaecsq/libraries.csv | 5 + .../jobs/ng2o8d1y_g4kzaifb/libraries.csv | 7 + .../ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb.cmd | 17 + .../ng2o8d1y_g4kzaifb/outs/summary.csv | 2 + .../ng2o8d1y_g4kzaifb/outs/web_summary.html | 324 ++++++++++++++++++ .../jobs/zoxefjul_5m23u91h/libraries.csv | 7 + .../zoxefjul_5m23u91h/zoxefjul_5m23u91h.cmd | 17 + .../zoxefjul_5m23u91h/outs/summary.csv | 2 + .../zoxefjul_5m23u91h/outs/web_summary.html | 324 ++++++++++++++++++ 16 files changed, 1397 insertions(+) create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou.cmd create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/summary.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/web_summary.html create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/libraries.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq.cmd create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/summary.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/web_summary.html create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/libraries.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/libraries.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb.cmd create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/summary.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/web_summary.html create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/libraries.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h.cmd create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/summary.csv create mode 100644 multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/web_summary.html diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou.cmd b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou.cmd new file mode 100644 index 0000000..0b0f204 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou.cmd @@ -0,0 +1,18 @@ +#!/bin/bash +#SBATCH --job-name="hagf3y16_sldip2ou" +#SBATCH --mail-type=all +#SBATCH --mail-user=ramon.massoni@cnag.crg.eu +#SBATCH --error=./log/hagf3y16_sldip2ou_%J.err +#SBATCH --output=./log/hagf3y16_sldip2ou_%J.out +#SBATCH -t 23:59:00 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH -q long +#SBATCH -p genD + + +echo [`date "+%Y-%m-%d %T"`] starting job on $HOSTNAME + +/scratch/groups/hheyn/software/cellranger-arc/1.0.0/cellranger-arc-1.0.0/cellranger-arc count --id hagf3y16_sldip2ou --reference /scratch/groups/hheyn/data/reference/refdata-cellranger-arc-GRCh38-2020-A --libraries libraries.csv; + +echo [`date "+%Y-%m-%d %T"`] job finished diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/summary.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/summary.csv new file mode 100644 index 0000000..f4a1375 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/summary.csv @@ -0,0 +1,2 @@ +Sample ID,Pipeline version,Genome,Estimated number of cells,ATAC Confidently mapped read pairs,ATAC Fraction of genome in peaks,ATAC Fraction of high-quality fragments in cells,ATAC Fraction of high-quality fragments overlapping TSS,ATAC Fraction of high-quality fragments overlapping peaks,ATAC Fraction of transposition events in peaks in cells,ATAC Mean raw read pairs per cell,ATAC Median high-quality fragments per cell,ATAC Non-nuclear read pairs,ATAC Number of peaks,ATAC Percent duplicates,ATAC Q30 bases in barcode,ATAC Q30 bases in read 1,ATAC Q30 bases in read 2,ATAC Q30 bases in sample index i1,ATAC Sequenced read pairs,ATAC TSS enrichment score,ATAC Unmapped read pairs,ATAC Valid barcodes,Feature linkages detected,GEX Fraction of transcriptomic reads in cells,GEX Mean raw reads per cell,GEX Median UMI counts per cell,GEX Median genes per cell,GEX Percent duplicates,GEX Q30 bases in UMI,GEX Q30 bases in barcode,GEX Q30 bases in read 2,GEX Reads mapped antisense to gene,GEX Reads mapped confidently to exonic regions,GEX Reads mapped confidently to genome,GEX Reads mapped confidently to intergenic regions,GEX Reads mapped confidently to intronic regions,GEX Reads mapped confidently to transcriptome,GEX Reads mapped to genome,GEX Reads with TSO,GEX Sequenced read pairs,GEX Total genes detected,GEX Valid UMIs,GEX Valid barcodes,Linked genes,Linked peaks +hagf3y16_sldip2ou,cellranger-arc-1.0.0,GRCh38,8662,0.81117,0.03424,0.80924,0.4605,0.69839,0.6811,24189.09444,6929,0.00245,89923,0.45785,0.90384,0.92987,0.92684,,209525936,10.37441,0.11747,0.97984,124146,0.84106,18421.60552,2912,1492.5,0.62189,0.93794,0.9455,0.91244,0.17492,0.4377,0.91833,0.06293,0.4177,0.67406,0.96906,0.05751,159567947,28283,0.99922,0.95554,9245,34601 diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/web_summary.html b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/web_summary.html new file mode 100644 index 0000000..023703c --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/hagf3y16_sldip2ou/outs/web_summary.html @@ -0,0 +1,324 @@ + + + + + + + + + +
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+ + + + + + diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/libraries.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/libraries.csv new file mode 100644 index 0000000..557b35a --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/libraries.csv @@ -0,0 +1,5 @@ +fastqs,sample,library_type +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/fastq/ATAC/lane2,hagf3y16_sldip2ou_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/fastq/ATAC/lane1,hagf3y16_sldip2ou_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/fastq/RNA/lane2,hagf3y16_sldip2ou_rna,Gene Expression +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/hagf3y16_sldip2ou/fastq/RNA/lane1,hagf3y16_sldip2ou_rna,Gene Expression \ No newline at end of file diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq.cmd b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq.cmd new file mode 100644 index 0000000..1bd77ea --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq.cmd @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name="k8s4gkxa_phcaecsq" +#SBATCH --mail-type=all +#SBATCH --mail-user=ramon.massoni@cnag.crg.eu +#SBATCH --error=./log/k8s4gkxa_phcaecsq_%x_%J.err +#SBATCH --output=./log/k8s4gkxa_phcaecsq_%x_%J.out +#SBATCH -t 23:59:00 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH -q long +#SBATCH -p genD + +echo [`date "+%Y-%m-%d %T"`] starting job on $HOSTNAME + +/scratch/groups/hheyn/software/cellranger-arc/1.0.0/cellranger-arc-1.0.0/cellranger-arc count --id k8s4gkxa_phcaecsq --reference /scratch/groups/hheyn/data/reference/refdata-cellranger-arc-GRCh38-2020-A --libraries libraries.csv; + +echo [`date "+%Y-%m-%d %T"`] job finished diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/summary.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/summary.csv new file mode 100644 index 0000000..64876d6 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/summary.csv @@ -0,0 +1,2 @@ +Sample ID,Pipeline version,Genome,Estimated number of cells,ATAC Confidently mapped read pairs,ATAC Fraction of genome in peaks,ATAC Fraction of high-quality fragments in cells,ATAC Fraction of high-quality fragments overlapping TSS,ATAC Fraction of high-quality fragments overlapping peaks,ATAC Fraction of transposition events in peaks in cells,ATAC Mean raw read pairs per cell,ATAC Median high-quality fragments per cell,ATAC Non-nuclear read pairs,ATAC Number of peaks,ATAC Percent duplicates,ATAC Q30 bases in barcode,ATAC Q30 bases in read 1,ATAC Q30 bases in read 2,ATAC Q30 bases in sample index i1,ATAC Sequenced read pairs,ATAC TSS enrichment score,ATAC Unmapped read pairs,ATAC Valid barcodes,Feature linkages detected,GEX Fraction of transcriptomic reads in cells,GEX Mean raw reads per cell,GEX Median UMI counts per cell,GEX Median genes per cell,GEX Percent duplicates,GEX Q30 bases in UMI,GEX Q30 bases in barcode,GEX Q30 bases in read 2,GEX Reads mapped antisense to gene,GEX Reads mapped confidently to exonic regions,GEX Reads mapped confidently to genome,GEX Reads mapped confidently to intergenic regions,GEX Reads mapped confidently to intronic regions,GEX Reads mapped confidently to transcriptome,GEX Reads mapped to genome,GEX Reads with TSO,GEX Sequenced read pairs,GEX Total genes detected,GEX Valid UMIs,GEX Valid barcodes,Linked genes,Linked peaks +k8s4gkxa_phcaecsq,cellranger-arc-1.0.0,GRCh38,9242,0.88034,0.03622,0.83258,0.46419,0.71091,0.6953,21341.70883,6840.5,0.00287,91125,0.46457,0.91324,0.93601,0.93182,,197240073,10.59646,0.04428,0.98268,137190,0.85005,21647.32861,3149.5,1587,0.65635,0.93522,0.94259,0.92398,0.17256,0.43874,0.91715,0.05927,0.41915,0.67899,0.96954,0.04208,200064611,28568,0.99906,0.95725,9638,36348 diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/web_summary.html b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/web_summary.html new file mode 100644 index 0000000..670ceda --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/k8s4gkxa_phcaecsq/outs/web_summary.html @@ -0,0 +1,324 @@ + + + + + + + + + +
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+ + + + + + diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/libraries.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/libraries.csv new file mode 100644 index 0000000..773d28a --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/libraries.csv @@ -0,0 +1,5 @@ +fastqs,sample,library_type +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/fastq/ATAC/lane2,k8s4gkxa_phcaecsq_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/fastq/ATAC/lane1,k8s4gkxa_phcaecsq_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/fastq/RNA/lane2,k8s4gkxa_phcaecsq_rna,Gene Expression +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/k8s4gkxa_phcaecsq/fastq/RNA/lane1,k8s4gkxa_phcaecsq_rna,Gene Expression \ No newline at end of file diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/libraries.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/libraries.csv new file mode 100644 index 0000000..47a3fb9 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/libraries.csv @@ -0,0 +1,7 @@ +fastqs,sample,library_type +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/fastq/ATAC/lane2,ng2o8d1y_g4kzaifb_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/fastq/ATAC/lane4,ng2o8d1y_g4kzaifb_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/fastq/ATAC/lane1,ng2o8d1y_g4kzaifb_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/fastq/ATAC/lane3,ng2o8d1y_g4kzaifb_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/fastq/RNA/lane2,ng2o8d1y_g4kzaifb_rna,Gene Expression +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/fastq/RNA/lane1,ng2o8d1y_g4kzaifb_rna,Gene Expression \ No newline at end of file diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb.cmd b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb.cmd new file mode 100644 index 0000000..93215eb --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb.cmd @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name="ng2o8d1y_g4kzaifb" +#SBATCH --mail-type=all +#SBATCH --mail-user=ramon.massoni@cnag.crg.eu +#SBATCH --error=./log/ng2o8d1y_g4kzaifb_%x_%J.err +#SBATCH --output=./log/ng2o8d1y_g4kzaifb_%x_%J.out +#SBATCH -t 23:59:00 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH -q long +#SBATCH -p genD + +echo [`date "+%Y-%m-%d %T"`] starting job on $HOSTNAME + +/scratch/groups/hheyn/software/cellranger-arc/1.0.0/cellranger-arc-1.0.0/cellranger-arc count --id ng2o8d1y_g4kzaifb --reference /scratch/groups/hheyn/data/reference/refdata-cellranger-arc-GRCh38-2020-A --libraries libraries.csv; + +echo [`date "+%Y-%m-%d %T"`] job finished diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/summary.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/summary.csv new file mode 100644 index 0000000..c38a95d --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/summary.csv @@ -0,0 +1,2 @@ +Sample ID,Pipeline version,Genome,Estimated number of cells,ATAC Confidently mapped read pairs,ATAC Fraction of genome in peaks,ATAC Fraction of high-quality fragments in cells,ATAC Fraction of high-quality fragments overlapping TSS,ATAC Fraction of high-quality fragments overlapping peaks,ATAC Fraction of transposition events in peaks in cells,ATAC Mean raw read pairs per cell,ATAC Median high-quality fragments per cell,ATAC Non-nuclear read pairs,ATAC Number of peaks,ATAC Percent duplicates,ATAC Q30 bases in barcode,ATAC Q30 bases in read 1,ATAC Q30 bases in read 2,ATAC Q30 bases in sample index i1,ATAC Sequenced read pairs,ATAC TSS enrichment score,ATAC Unmapped read pairs,ATAC Valid barcodes,Feature linkages detected,GEX Fraction of transcriptomic reads in cells,GEX Mean raw reads per cell,GEX Median UMI counts per cell,GEX Median genes per cell,GEX Percent duplicates,GEX Q30 bases in UMI,GEX Q30 bases in barcode,GEX Q30 bases in read 2,GEX Reads mapped antisense to gene,GEX Reads mapped confidently to exonic regions,GEX Reads mapped confidently to genome,GEX Reads mapped confidently to intergenic regions,GEX Reads mapped confidently to intronic regions,GEX Reads mapped confidently to transcriptome,GEX Reads mapped to genome,GEX Reads with TSO,GEX Sequenced read pairs,GEX Total genes detected,GEX Valid UMIs,GEX Valid barcodes,Linked genes,Linked peaks +ng2o8d1y_g4kzaifb,cellranger-arc-1.0.0,GRCh38,8565,0.85328,0.02061,0.57746,0.40627,0.57314,0.5559,23792.27215,6629,0.00652,66099,0.36081,0.9129,0.9436,0.93812,,203780811,9.18536,0.05117,0.98164,53692,0.85371,22799.15295,3730,1731,0.64543,0.93911,0.94684,0.93747,0.145,0.34437,0.9169,0.09128,0.48125,0.67324,0.96154,0.07333,195274745,29142,0.9994,0.95458,5917,17060 diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/web_summary.html b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/web_summary.html new file mode 100644 index 0000000..dd51b66 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/ng2o8d1y_g4kzaifb/ng2o8d1y_g4kzaifb/outs/web_summary.html @@ -0,0 +1,324 @@ + + + + + + + + + +
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+ + + + + + diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/libraries.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/libraries.csv new file mode 100644 index 0000000..4acc0e6 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/libraries.csv @@ -0,0 +1,7 @@ +fastqs,sample,library_type +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/fastq/ATAC/lane2,zoxefjul_5m23u91h_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/fastq/ATAC/lane4,zoxefjul_5m23u91h_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/fastq/ATAC/lane1,zoxefjul_5m23u91h_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/fastq/ATAC/lane3,zoxefjul_5m23u91h_atac,Chromatin Accessibility +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/fastq/RNA/lane2,zoxefjul_5m23u91h_rna,Gene Expression +/scratch/devel/rmassoni/tonsil_atlas/current/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/fastq/RNA/lane1,zoxefjul_5m23u91h_rna,Gene Expression \ No newline at end of file diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h.cmd b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h.cmd new file mode 100644 index 0000000..dcaabdc --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h.cmd @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name="zoxefjul_5m23u91h" +#SBATCH --mail-type=all +#SBATCH --mail-user=ramon.massoni@cnag.crg.eu +#SBATCH --error=./log/zoxefjul_5m23u91h_%x_%J.err +#SBATCH --output=./log/zoxefjul_5m23u91h_%x_%J.out +#SBATCH -t 23:59:00 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH -q long +#SBATCH -p genD + +echo [`date "+%Y-%m-%d %T"`] starting job on $HOSTNAME + +/scratch/groups/hheyn/software/cellranger-arc/1.0.0/cellranger-arc-1.0.0/cellranger-arc count --id zoxefjul_5m23u91h --reference /scratch/groups/hheyn/data/reference/refdata-cellranger-arc-GRCh38-2020-A --libraries libraries.csv; + +echo [`date "+%Y-%m-%d %T"`] job finished diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/summary.csv b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/summary.csv new file mode 100644 index 0000000..e01411d --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/summary.csv @@ -0,0 +1,2 @@ +Sample ID,Pipeline version,Genome,Estimated number of cells,ATAC Confidently mapped read pairs,ATAC Fraction of genome in peaks,ATAC Fraction of high-quality fragments in cells,ATAC Fraction of high-quality fragments overlapping TSS,ATAC Fraction of high-quality fragments overlapping peaks,ATAC Fraction of transposition events in peaks in cells,ATAC Mean raw read pairs per cell,ATAC Median high-quality fragments per cell,ATAC Non-nuclear read pairs,ATAC Number of peaks,ATAC Percent duplicates,ATAC Q30 bases in barcode,ATAC Q30 bases in read 1,ATAC Q30 bases in read 2,ATAC Q30 bases in sample index i1,ATAC Sequenced read pairs,ATAC TSS enrichment score,ATAC Unmapped read pairs,ATAC Valid barcodes,Feature linkages detected,GEX Fraction of transcriptomic reads in cells,GEX Mean raw reads per cell,GEX Median UMI counts per cell,GEX Median genes per cell,GEX Percent duplicates,GEX Q30 bases in UMI,GEX Q30 bases in barcode,GEX Q30 bases in read 2,GEX Reads mapped antisense to gene,GEX Reads mapped confidently to exonic regions,GEX Reads mapped confidently to genome,GEX Reads mapped confidently to intergenic regions,GEX Reads mapped confidently to intronic regions,GEX Reads mapped confidently to transcriptome,GEX Reads mapped to genome,GEX Reads with TSO,GEX Sequenced read pairs,GEX Total genes detected,GEX Valid UMIs,GEX Valid barcodes,Linked genes,Linked peaks +zoxefjul_5m23u91h,cellranger-arc-1.0.0,GRCh38,9215,0.86412,0.02224,0.60577,0.40761,0.58301,0.56323,23460.32306,6735,0.00647,67534,0.37078,0.91501,0.93558,0.93262,,216186877,9.01343,0.04374,0.98191,64361,0.86039,23809.97645,3626,1716,0.6868,0.9354,0.94255,0.93431,0.13425,0.34655,0.91883,0.08192,0.49037,0.69487,0.96318,0.05954,219408933,29114,0.99938,0.95805,6499,19105 diff --git a/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/web_summary.html b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/web_summary.html new file mode 100644 index 0000000..95e4980 --- /dev/null +++ b/multiome/1-cellranger_mapping/projects/experiment_3/jobs/zoxefjul_5m23u91h/zoxefjul_5m23u91h/outs/web_summary.html @@ -0,0 +1,324 @@ + + + + + + + + + +
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