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‎.gitignore‎

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@@ -5,4 +5,5 @@ temp/*
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scratch/*
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manual-inspection/hashtag/*
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manual-inspection/citeseq/*
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config/*
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configs/archive/*
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configs/sanity-check/*

‎README.md‎

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## Setup
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```bash
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aws s3 cp s3://dp-lab-home/software/install-sharp-0.0.5.sh - | bash
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aws s3 cp s3://dp-lab-home/software/install-sharp-0.0.6.sh - | bash
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```
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```
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./submit-hashtag.sh \
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-k ~/secrets-aws.json \
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-i config/PBMC_v2_Meth_Hash_2_ADT.inputs.json \
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-l config/PBMC_v2_Meth_Hash_2_ADT.labels.json \
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-i configs/PBMC_v2_Meth_Hash_2_ADT.inputs.json \
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-l configs/PBMC_v2_Meth_Hash_2_ADT.labels.json \
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-o Sharp.options.aws.json
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```
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./submit-citeseq.sh \
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-k ~/secrets-aws.json \
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-i config/PBMC_v2_Meth_Hash_2_ADT.inputs.json \
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-l config/PBMC_v2_Meth_Hash_2_ADT.labels.json \
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-i configs/PBMC_v2_Meth_Hash_2_ADT.inputs.json \
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-l configs/PBMC_v2_Meth_Hash_2_ADT.labels.json \
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-o Sharp.options.aws.json
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```
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‎Sharp.deps.zip‎

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‎config/IL10neg.inputs.json‎

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‎configs/citeseq.inputs.json‎

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{
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"CiteSeq.uriFastqR1": [
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L001_R1_001.fastq.gz",
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L002_R1_001.fastq.gz",
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/FASTQ/2090_CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L001_R1_001.fastq.gz",
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/FASTQ/2090_CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L002_R1_001.fastq.gz"
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],
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"CiteSeq.uriFastqR2": [
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L001_R2_001.fastq.gz",
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L002_R2_001.fastq.gz",
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/FASTQ/2090_CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L001_R2_001.fastq.gz",
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"s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/FASTQ/2090_CS1429a_T_1_CD45pos_citeseq_1_CITE_IGO_11242_11_S17_L002_R2_001.fastq.gz"
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],
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"CiteSeq.sampleName": "2090_CS1429a_T_1_CD45pos_citeseq_1_CITE",
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"CiteSeq.scRnaSeqPlatform": "10x_v3",
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"CiteSeq.lengthR1": 28,
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"CiteSeq.lengthR2": 15,
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"CiteSeq.cellBarcodeWhitelistUri": "s3://dp-lab-data/SCRI_Projects/HTAN_CITEseq/CS1429a_T_1_CD45pos_citeseq_1/seqc-results/2090_CS1429a_T_1_CD45pos_citeseq_1_IGO_11244_17_dense.csv",
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"CiteSeq.cellBarcodeWhiteListMethod": "SeqcDenseCountsMatrixCsv",
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"CiteSeq.tagList": "s3://dp-lab-data/sc-seq/Project_11242/CS1429a_T_1_CD45pos_citeseq_1_CITE/Hashtag_results/tag-list.csv",
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"CiteSeq.cbStartPos": 1,
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"CiteSeq.cbEndPos": 16,
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"CiteSeq.umiStartPos": 17,
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"CiteSeq.umiEndPos": 28,
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"CiteSeq.trimPos": 0,
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"CiteSeq.slidingWindowSearch": false,
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"CiteSeq.translate10XBarcodes": false,
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"CiteSeq.cbCollapsingDistance": 1,
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"CiteSeq.umiCollapsingDistance": 1,
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"CiteSeq.numExpectedCells": 0,
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"CiteSeq.denseCountMatrix": "s3://dp-lab-data/SCRI_Projects/HTAN_CITEseq/CS1429a_T_1_CD45pos_citeseq_1/seqc-results/2090_CS1429a_T_1_CD45pos_citeseq_1_IGO_11244_17_dense.csv",
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"CiteSeq.resourceSpec": {
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"cpu": 4,
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"memory": 64
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}
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}

‎configs/citeseq.labels.json‎

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{
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"pipelineType": "CITE-seq",
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"project": "Project 230",
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"sample": "2090_CS1429a_T_1_CD45pos_citeseq_1_CITE",
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"owner": "chunj",
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"destination": "s3://dp-lab-test/sharp/citeseq/",
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"transfer": "-",
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"comment": "CITE-seq"
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}

config/IL10pos.inputs.json renamed to configs/hashtag-10x-v3-totalseq-A.inputs.json

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‎configs/hashtag-10x-v3-totalseq-A.labels.json‎

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{
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"pipelineType": "Sharp",
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"project": "Project 10034",
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"sample": "IL10pos",
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"owner": "chunj",
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"destination": "s3://dp-lab-test/sharp/hashtag/10x-v3-totalseq-A/",
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"transfer": "-",
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"comment": "10x v3 TotalSeq-A"
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}

‎configs/hashtag-10x-v3-totalseq-B.inputs.json‎

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{
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"Sharp.uriFastqR1": [
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"s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK_FB_HTO/FASTQ/HD1915_7xNK_FB_IGO_10657_B_2_S2_L001_R1_001.fastq.gz",
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"s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK_FB_HTO/FASTQ/HD1915_7xNK_FB_IGO_10657_B_2_S2_L002_R1_001.fastq.gz"
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],
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"Sharp.uriFastqR2": [
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"s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK_FB_HTO/FASTQ/HD1915_7xNK_FB_IGO_10657_B_2_S2_L001_R2_001.fastq.gz",
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"s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK_FB_HTO/FASTQ/HD1915_7xNK_FB_IGO_10657_B_2_S2_L002_R2_001.fastq.gz"
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],
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"Sharp.sampleName": "1973_HD1915_7xNK_FB_HTO",
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"Sharp.scRnaSeqPlatform": "10x_v3",
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"Sharp.lengthR1": 28,
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"Sharp.lengthR2": 25,
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"Sharp.cellBarcodeWhitelistUri": "s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK/seqc-results/1973_HD1915_7xNK_IGO_10657_2_dense.csv",
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"Sharp.cellBarcodeWhiteListMethod": "SeqcDenseCountsMatrixCsv",
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"Sharp.translate10XBarcodes": true,
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"Sharp.hashTagList": "s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK_FB_HTO/Hashtag_results/tag-list.csv",
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"Sharp.cbStartPos": 1,
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"Sharp.cbEndPos": 16,
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"Sharp.umiStartPos": 17,
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"Sharp.umiEndPos": 28,
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"Sharp.trimPos": 10,
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"Sharp.slidingWindowSearch": false,
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"Sharp.cbCollapsingDistance": 1,
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"Sharp.umiCollapsingDistance": 1,
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"Sharp.numExpectedCells": 0,
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"Sharp.denseCountMatrix": "s3://dp-lab-data/collaborators/hsuk/7xNK/HD1915_7xNK/seqc-results/1973_HD1915_7xNK_IGO_10657_2_dense.csv",
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"Sharp.resourceSpec": {
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"cpu": 32,
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"memory": 64
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}
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}

‎configs/hashtag-10x-v3-totalseq-B.labels.json‎

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{
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"pipelineType": "Sharp",
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"project": "Project 226",
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"sample": "1973_HD1915_7xNK_FB_HTO",
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"owner": "chunj",
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"destination": "s3://dp-lab-test/sharp/hashtag/10x-v3-totalseq-B/",
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"transfer": "-",
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"comment": "10x v3 TotalSeq-B"
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}

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