From f140f6cbe3ef2c50bf84dff0b020b93fdeafcdba Mon Sep 17 00:00:00 2001 From: "Matthew A. Wyczalkowski" Date: Fri, 25 Feb 2022 11:56:52 -0600 Subject: [PATCH] Import of LUAD RNA-Seq to katmai, batch 20220224.LUAD19 * .12906003 Tb in 19 files, 18 RNA-Seq, 1 miRNA * RNA seems to have duplicate sample name. May be associated with Gencode v36 * Not clear how to distinguish gencode version differences * Download workdir: /home/mwyczalk_test/Projects/CPTAC3/import.Y3/20220224.LUAD19 * UUID discovery and data: shiso:/Users/mwyczalk/Projects/CPTAC3/CPTAC3.Cases/20220222.LUAD_CaseUpdate/CPTAC3.MissingAnalysis/dat/downloads/katmai.download_UUID.dat --- BamMap/katmai.BamMap.dat | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/BamMap/katmai.BamMap.dat b/BamMap/katmai.BamMap.dat index 3bf9c19..b071ed1 100644 --- a/BamMap/katmai.BamMap.dat +++ b/BamMap/katmai.BamMap.dat @@ -1817,7 +1817,9 @@ C3L-00973.MethArray.Red.T C3L-00973 LUAD Methylation Array tumor /diskmnt/Projec C3L-00973.miRNA-Seq.A C3L-00973 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/fd7e0fc5-d407-44ea-b8a0-0c8d7b483787/181108_UNC31-K00269_0163_BH23TVBBXY_TACAGC_S43_L002_R1_001.unaln.bam 183330432 BAM NA fd7e0fc5-d407-44ea-b8a0-0c8d7b483787 katmai C3L-00973.miRNA-Seq.T C3L-00973 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/faf5b1f6-a765-4f43-ad06-3b0f9e33bfc1/181113_UNC31-K00269_0164_AH23NNBBXY_ACTTGA_S32_L002_R1_001.unaln.bam 201419237 BAM NA faf5b1f6-a765-4f43-ad06-3b0f9e33bfc1 katmai C3L-00973.RNA-Seq.genomic.A.hg38 C3L-00973 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/0f768cdb-054f-4be8-b40e-fa42c0b268e4/028320b3-78b3-4db8-a4c0-d6135c74e1c7.rna_seq.genomic.gdc_realn.bam 6628198009 BAM hg38 0f768cdb-054f-4be8-b40e-fa42c0b268e4 katmai +C3L-00973.RNA-Seq.genomic.A.hg38 C3L-00973 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/defc6691-7b01-42ec-bc76-91a4509ed514/8c0be93f-de25-4bfe-abb3-ae3840bc40c2.rna_seq.genomic.gdc_realn.bam 6629267678 BAM hg38 defc6691-7b01-42ec-bc76-91a4509ed514 katmai C3L-00973.RNA-Seq.genomic.T.hg38 C3L-00973 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/6e081d4e-40b9-4011-85bb-229d301747ed/096ec9ed-3053-4e94-8c5d-e672115a807f.rna_seq.genomic.gdc_realn.bam 8907462848 BAM hg38 6e081d4e-40b9-4011-85bb-229d301747ed katmai +C3L-00973.RNA-Seq.genomic.T.hg38 C3L-00973 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/b60d8059-170b-4bd8-b621-e365cbe8cb6b/38eeb9a9-221f-4360-8000-8264f8919b4c.rna_seq.genomic.gdc_realn.bam 8909848053 BAM hg38 b60d8059-170b-4bd8-b621-e365cbe8cb6b katmai C3L-00973.RNA-Seq.R1.A C3L-00973 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/6afb7982-855b-4f29-8cb9-65348024e16b/171215_UNC32-K00270_0072_AHN3THBBXX_GTGGCC_S19_L005_R1_001.fastq.gz 3382647784 FASTQ NA 6afb7982-855b-4f29-8cb9-65348024e16b katmai C3L-00973.RNA-Seq.R1.T C3L-00973 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/dde76172-11ea-42ed-b376-abb20a41fcbd/171109_UNC31-K00269_0090_AHLHNWBBXX_ACTGAT_S8_L002_R1_001.fastq.gz 4080024026 FASTQ NA dde76172-11ea-42ed-b376-abb20a41fcbd katmai C3L-00973.RNA-Seq.R2.A C3L-00973 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/8a6f24e8-d172-4d34-a3a5-34aaf06cc554/171215_UNC32-K00270_0072_AHN3THBBXX_GTGGCC_S19_L005_R2_001.fastq.gz 3570586126 FASTQ NA 8a6f24e8-d172-4d34-a3a5-34aaf06cc554 katmai @@ -3709,7 +3711,9 @@ C3L-02348.MethArray.Red.T C3L-02348 LUAD Methylation Array tumor /diskmnt/Projec C3L-02348.miRNA-Seq.A C3L-02348 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/5e0058e3-b20f-4ca2-bf7f-bb578fcca5e2/181108_UNC31-K00269_0162_AH255GBBXY_TCCCGA_S22_L005_R1_001.unaln.bam 211877763 BAM NA 5e0058e3-b20f-4ca2-bf7f-bb578fcca5e2 katmai C3L-02348.miRNA-Seq.T C3L-02348 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/0a9a41f2-9374-40fc-b5c2-1a506c697d79/181119_UNC31-K00269_0165_AH27WCBBXY_GGTAGC_S48_L003_R1_001.unaln.bam 203229394 BAM NA 0a9a41f2-9374-40fc-b5c2-1a506c697d79 katmai C3L-02348.RNA-Seq.genomic.A.hg38 C3L-02348 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/9e6f7ec6-a7b5-4a76-a922-cf519679c8b0/a0c3f1e9-c0f9-4d57-a1d3-7a0f35f52e7c.rna_seq.genomic.gdc_realn.bam 8943245316 BAM hg38 9e6f7ec6-a7b5-4a76-a922-cf519679c8b0 katmai +C3L-02348.RNA-Seq.genomic.A.hg38 C3L-02348 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/116efeb3-7a31-45e5-b992-66011a9afda4/561feb2e-d7fd-4bcc-88ca-16d67dfd2d27.rna_seq.genomic.gdc_realn.bam 8944078812 BAM hg38 116efeb3-7a31-45e5-b992-66011a9afda4 katmai C3L-02348.RNA-Seq.genomic.T.hg38 C3L-02348 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/e8ff44d0-8fd2-42c2-8adf-95391771f081/6a14fe1c-8d7e-4c09-864c-9d1a916da793.rna_seq.genomic.gdc_realn.bam 9313257135 BAM hg38 e8ff44d0-8fd2-42c2-8adf-95391771f081 katmai +C3L-02348.RNA-Seq.genomic.T.hg38 C3L-02348 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/2414e46e-bb32-4989-a6cf-c61cfce1f008/8e11e2bc-d024-4ec1-bf4e-b2844df53166.rna_seq.genomic.gdc_realn.bam 9314992269 BAM hg38 2414e46e-bb32-4989-a6cf-c61cfce1f008 katmai C3L-02348.RNA-Seq.R1.A C3L-02348 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/1cdf25ca-920c-4f76-8bcf-6b55a52862cf/171215_UNC32-K00270_0073_BHN3NFBBXX_GAGTGG_S1_L001_R1_001.fastq.gz 4270003276 FASTQ NA 1cdf25ca-920c-4f76-8bcf-6b55a52862cf katmai C3L-02348.RNA-Seq.R1.T C3L-02348 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/ae598f4f-e0d0-408b-95af-5a66f66806e2/171109_UNC31-K00269_0091_BHMFGTBBXX_CGATGT_S10_L003_R1_001.fastq.gz 4340031904 FASTQ NA ae598f4f-e0d0-408b-95af-5a66f66806e2 katmai C3L-02348.RNA-Seq.R2.A C3L-02348 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/a8c23156-1897-4834-8e25-5be6c4e53be7/171215_UNC32-K00270_0073_BHN3NFBBXX_GAGTGG_S1_L001_R2_001.fastq.gz 4696678825 FASTQ NA a8c23156-1897-4834-8e25-5be6c4e53be7 katmai @@ -3731,7 +3735,9 @@ C3L-02350.MethArray.Red.T C3L-02350 LUAD Methylation Array tumor /diskmnt/Projec C3L-02350.miRNA-Seq.A C3L-02350 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/39e39838-395d-4454-8721-c5caf1f9bfe7/181108_UNC31-K00269_0162_AH255GBBXY_CGGAAT_S13_L007_R1_001.unaln.bam 237909545 BAM NA 39e39838-395d-4454-8721-c5caf1f9bfe7 katmai C3L-02350.miRNA-Seq.T C3L-02350 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/66a007ac-96dc-42d1-951c-5ad8bafa7a09/181108_UNC31-K00269_0163_BH23TVBBXY_GACGAC_S41_L007_R1_001.unaln.bam 235654598 BAM NA 66a007ac-96dc-42d1-951c-5ad8bafa7a09 katmai C3L-02350.RNA-Seq.genomic.A.hg38 C3L-02350 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/fbb501da-459b-4046-880b-7f28c6a49be7/72843144-5c79-482c-9307-ae76a69c3007.rna_seq.genomic.gdc_realn.bam 8404897132 BAM hg38 fbb501da-459b-4046-880b-7f28c6a49be7 katmai +C3L-02350.RNA-Seq.genomic.A.hg38 C3L-02350 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/f6cde4c4-3e31-4128-83e4-bee6b3152f06/efd7b9eb-0e43-473c-8b68-e8f2dba08dda.rna_seq.genomic.gdc_realn.bam 8405764202 BAM hg38 f6cde4c4-3e31-4128-83e4-bee6b3152f06 katmai C3L-02350.RNA-Seq.genomic.T.hg38 C3L-02350 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/7f253b89-149f-43c8-bf28-56f00d58191c/f307f2f8-e763-4961-b754-104b2d41a652.rna_seq.genomic.gdc_realn.bam 9802660718 BAM hg38 7f253b89-149f-43c8-bf28-56f00d58191c katmai +C3L-02350.RNA-Seq.genomic.T.hg38 C3L-02350 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/4b4918de-9d15-42d9-8c72-656fd1095ee3/2b519912-61c7-4104-b5d4-7a26beb73fd7.rna_seq.genomic.gdc_realn.bam 9805706221 BAM hg38 4b4918de-9d15-42d9-8c72-656fd1095ee3 katmai C3L-02350.RNA-Seq.R1.A C3L-02350 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/33fc37f3-73e1-4159-8e52-3be53dd9e2c3/171215_UNC32-K00270_0073_BHN3NFBBXX_AGTCAA_S16_L004_R1_001.fastq.gz 3967363449 FASTQ NA 33fc37f3-73e1-4159-8e52-3be53dd9e2c3 katmai C3L-02350.RNA-Seq.R1.T C3L-02350 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/82879494-5e4b-463c-bd21-c7f0f17a0f48/171109_UNC31-K00269_0090_AHLHNWBBXX_CAGATC_S21_L006_R1_001.fastq.gz 4372927334 FASTQ NA 82879494-5e4b-463c-bd21-c7f0f17a0f48 katmai C3L-02350.RNA-Seq.R2.A C3L-02350 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/a09255be-5c21-4ef8-a02d-f2639f19ed6e/171215_UNC32-K00270_0073_BHN3NFBBXX_AGTCAA_S16_L004_R2_001.fastq.gz 4451962157 FASTQ NA a09255be-5c21-4ef8-a02d-f2639f19ed6e katmai @@ -6659,7 +6665,9 @@ C3N-00545.MethArray.Red.T.RDNA_omG0EN C3N-00545 LUAD Methylation Array tumor /di C3N-00545.miRNA-Seq.A C3N-00545 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/46632a8c-d298-443e-9958-5b7c9b910d38/181108_UNC31-K00269_0162_AH255GBBXY_GGCTAC_S35_L008_R1_001.unaln.bam 340074823 BAM NA 46632a8c-d298-443e-9958-5b7c9b910d38 katmai C3N-00545.miRNA-Seq.T.RRNA_rpLvQk C3N-00545 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/c0690cda-cbfa-4206-826d-9c91903e4802/181113_UNC31-K00269_0164_AH23NNBBXY_CAGGCG_S9_L005_R1_001.unaln.bam 223125879 BAM NA c0690cda-cbfa-4206-826d-9c91903e4802 katmai C3N-00545.RNA-Seq.genomic.A.hg38 C3N-00545 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/1f83a85b-24a5-4ab4-a8b9-3ae42f66545d/a1aa06bc-8d65-41cf-a7fb-e2d413871405.rna_seq.genomic.gdc_realn.bam 7241206371 BAM hg38 1f83a85b-24a5-4ab4-a8b9-3ae42f66545d katmai +C3N-00545.RNA-Seq.genomic.A.hg38 C3N-00545 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/33070af6-ba41-4e3c-a946-69077e234f34/db9ea6d1-dff0-41ca-80cf-b890e67242bd.rna_seq.genomic.gdc_realn.bam 7241924520 BAM hg38 33070af6-ba41-4e3c-a946-69077e234f34 katmai C3N-00545.RNA-Seq.genomic.T.RRNA_rpLvQk.hg38 C3N-00545 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/1649b854-643b-4df6-9540-d9ea3c4f7a4e/c6758665-5587-4e98-97cd-139d22b31048.rna_seq.genomic.gdc_realn.bam 7222940788 BAM hg38 1649b854-643b-4df6-9540-d9ea3c4f7a4e katmai +C3N-00545.RNA-Seq.genomic.T.RRNA_rpLvQk.hg38 C3N-00545 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/b5c06561-24f7-46ac-a3bf-f4b376b6ac2e/84e5be7a-ba48-4c9e-9832-d93530662cc6.rna_seq.genomic.gdc_realn.bam 7224136868 BAM hg38 b5c06561-24f7-46ac-a3bf-f4b376b6ac2e katmai C3N-00546.MethArray.Green.A C3N-00546 LUAD Methylation Array tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/a3d97d6d-d189-464f-bff9-e0ebdaccc35d/203027390034_R05C01_Grn.idat 13676226 IDAT NA a3d97d6d-d189-464f-bff9-e0ebdaccc35d katmai C3N-00546.MethArray.Green.T C3N-00546 LUAD Methylation Array tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/72ac824e-fcb0-4f7c-a16a-7c2c9f5f47b3/202184900105_R05C01_Grn.idat 13676223 IDAT NA 72ac824e-fcb0-4f7c-a16a-7c2c9f5f47b3 katmai C3N-00546.MethArray.Red.A C3N-00546 LUAD Methylation Array tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/b4424c55-7db1-42de-a2b9-d8d9c39162c0/203027390034_R05C01_Red.idat 13676226 IDAT NA b4424c55-7db1-42de-a2b9-d8d9c39162c0 katmai @@ -7043,7 +7051,9 @@ C3N-00738.MethArray.Red.T C3N-00738 LUAD Methylation Array tumor /diskmnt/Projec C3N-00738.miRNA-Seq.A C3N-00738 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/978ed708-acdc-413f-92cb-6b402283d225/181108_UNC31-K00269_0162_AH255GBBXY_AGTCAA_S37_L008_R1_001.unaln.bam 245046421 BAM NA 978ed708-acdc-413f-92cb-6b402283d225 katmai C3N-00738.miRNA-Seq.T C3N-00738 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/03d631d0-ad05-40ba-b558-fb3d4e92027b/181113_UNC31-K00269_0164_AH23NNBBXY_CTTGTA_S36_L002_R1_001.unaln.bam 299660493 BAM NA 03d631d0-ad05-40ba-b558-fb3d4e92027b katmai C3N-00738.RNA-Seq.genomic.A.hg38 C3N-00738 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/3cd8ec7c-14ce-4f7c-bc34-d29ee7e9cd20/acc298b9-56b6-44ab-9723-f03a9c4bdc45.rna_seq.genomic.gdc_realn.bam 8502207562 BAM hg38 3cd8ec7c-14ce-4f7c-bc34-d29ee7e9cd20 katmai +C3N-00738.RNA-Seq.genomic.A.hg38 C3N-00738 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/5d0f1a8b-8ea6-42c8-a8a6-3fec8d799b54/ce3ed392-b8bb-4f54-9718-7bae5b148d63.rna_seq.genomic.gdc_realn.bam 8503007402 BAM hg38 5d0f1a8b-8ea6-42c8-a8a6-3fec8d799b54 katmai C3N-00738.RNA-Seq.genomic.T.hg38 C3N-00738 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/496b6d6e-5b59-4e8a-b258-50c14d041e20/d906f2da-c366-4347-8d11-5847d8491291.rna_seq.genomic.gdc_realn.bam 9403441077 BAM hg38 496b6d6e-5b59-4e8a-b258-50c14d041e20 katmai +C3N-00738.RNA-Seq.genomic.T.hg38 C3N-00738 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/b8858116-03a6-4a21-9599-cf2f0d1e1be7/65575a51-6350-4bf5-96b8-ca2062fbf511.rna_seq.genomic.gdc_realn.bam 9410522822 BAM hg38 b8858116-03a6-4a21-9599-cf2f0d1e1be7 katmai C3N-00738.RNA-Seq.R1.A C3N-00738 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/b8e3505e-43ad-4883-99b3-fc6b1db5630a/180103_UNC31-K00269_0105_AHNFGGBBXX_AGTCAA_S80_L008_R1_001.fastq.gz 4068920168 FASTQ NA b8e3505e-43ad-4883-99b3-fc6b1db5630a katmai C3N-00738.RNA-Seq.R1.T C3N-00738 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/c03373bb-4980-4327-af54-3ce878036954/171109_UNC31-K00269_0091_BHMFGTBBXX_GTCCGC_S18_L005_R1_001.fastq.gz 3825955251 FASTQ NA c03373bb-4980-4327-af54-3ce878036954 katmai C3N-00738.RNA-Seq.R2.A C3N-00738 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/ceddd54a-d07f-49ea-a755-4a0ea3be8eb9/180103_UNC31-K00269_0105_AHNFGGBBXX_AGTCAA_S80_L008_R2_001.fastq.gz 4363912702 FASTQ NA ceddd54a-d07f-49ea-a755-4a0ea3be8eb9 katmai @@ -7497,7 +7507,9 @@ C3N-01023.MethArray.Red.T C3N-01023 LUAD Methylation Array tumor /diskmnt/Projec C3N-01023.miRNA-Seq.A C3N-01023 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/8b3f6917-546b-43f1-83b4-90735f096d31/181108_UNC31-K00269_0162_AH255GBBXY_AGTTCC_S38_L008_R1_001.unaln.bam 218716852 BAM NA 8b3f6917-546b-43f1-83b4-90735f096d31 katmai C3N-01023.miRNA-Seq.T C3N-01023 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/68013eed-bcd2-4e0b-8142-212eb113caa0/181119_UNC31-K00269_0165_AH27WCBBXY_TCGAAG_S23_L005_R1_001.unaln.bam 197547821 BAM NA 68013eed-bcd2-4e0b-8142-212eb113caa0 katmai C3N-01023.RNA-Seq.genomic.A.hg38 C3N-01023 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/6f59bad9-48db-4f0a-b96a-0f76e7cfe3a0/c2d65d03-a8f9-4fd5-884e-0a180ffb06a9.rna_seq.genomic.gdc_realn.bam 8988416581 BAM hg38 6f59bad9-48db-4f0a-b96a-0f76e7cfe3a0 katmai +C3N-01023.RNA-Seq.genomic.A.hg38 C3N-01023 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/2bcfb2fa-4a70-44f5-ba46-ec5a8208f718/c26fcc72-38f9-4688-8b6c-74be78aa2fa0.rna_seq.genomic.gdc_realn.bam 8989705099 BAM hg38 2bcfb2fa-4a70-44f5-ba46-ec5a8208f718 katmai C3N-01023.RNA-Seq.genomic.T.hg38 C3N-01023 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/9d0f99f1-b7fb-4c06-b07d-3b0f84407146/0b12b3e1-c797-403c-931a-ded1f7179eb9.rna_seq.genomic.gdc_realn.bam 8969145110 BAM hg38 9d0f99f1-b7fb-4c06-b07d-3b0f84407146 katmai +C3N-01023.RNA-Seq.genomic.T.hg38 C3N-01023 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/efe9fea9-bffa-463b-9bcb-e1379ec8121a/21c41b6d-47ba-462d-bab6-b12792779020.rna_seq.genomic.gdc_realn.bam 8970092447 BAM hg38 efe9fea9-bffa-463b-9bcb-e1379ec8121a katmai C3N-01023.RNA-Seq.R1.A C3N-01023 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/68280a88-e5ab-4692-be16-13a8b89ab24c/171215_UNC32-K00270_0073_BHN3NFBBXX_AGTTCC_S10_L008_R1_001.fastq.gz 4245927775 FASTQ NA 68280a88-e5ab-4692-be16-13a8b89ab24c katmai C3N-01023.RNA-Seq.R1.T C3N-01023 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/58f7c30a-a7cd-44e3-91c6-db892b584c1c/171109_UNC31-K00269_0090_AHLHNWBBXX_AGTCAA_S15_L004_R1_001.fastq.gz 3885047829 FASTQ NA 58f7c30a-a7cd-44e3-91c6-db892b584c1c katmai C3N-01023.RNA-Seq.R2.A C3N-01023 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/18ae465e-5ade-4c9e-9d5e-fe5dbd18deb8/171215_UNC32-K00270_0073_BHN3NFBBXX_AGTTCC_S10_L008_R2_001.fastq.gz 4678324312 FASTQ NA 18ae465e-5ade-4c9e-9d5e-fe5dbd18deb8 katmai @@ -7509,7 +7521,9 @@ C3N-01024.MethArray.Red.T C3N-01024 LUAD Methylation Array tumor /diskmnt/Projec C3N-01024.miRNA-Seq.A C3N-01024 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/88413f59-2f60-4d4a-80e9-a9b27285ff75/181108_UNC31-K00269_0162_AH255GBBXY_CATTTT_S11_L007_R1_001.unaln.bam 233666891 BAM NA 88413f59-2f60-4d4a-80e9-a9b27285ff75 katmai C3N-01024.miRNA-Seq.T C3N-01024 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/2a551037-c6e8-4b98-a021-f69ce98a5f47/181108_UNC31-K00269_0163_BH23TVBBXY_TAATCG_S42_L007_R1_001.unaln.bam 180552171 BAM NA 2a551037-c6e8-4b98-a021-f69ce98a5f47 katmai C3N-01024.RNA-Seq.genomic.A.hg38 C3N-01024 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/aafc022d-92eb-4cd9-97a0-65cbfcc1abf1/b932f072-6f6e-4855-96c0-0782d5080c16.rna_seq.genomic.gdc_realn.bam 8851146595 BAM hg38 aafc022d-92eb-4cd9-97a0-65cbfcc1abf1 katmai +C3N-01024.RNA-Seq.genomic.A.hg38 C3N-01024 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/1fcb92f2-183d-48ad-84d3-4c2c9def7254/7e7e9c66-4e5e-459d-a16d-755fa7d53007.rna_seq.genomic.gdc_realn.bam 8852890117 BAM hg38 1fcb92f2-183d-48ad-84d3-4c2c9def7254 katmai C3N-01024.RNA-Seq.genomic.T.hg38 C3N-01024 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/cb3ed714-5d55-44bf-988b-b041bff49117/2a23ea8f-2aaa-4dc1-a400-23f3e134b08c.rna_seq.genomic.gdc_realn.bam 7102912027 BAM hg38 cb3ed714-5d55-44bf-988b-b041bff49117 katmai +C3N-01024.RNA-Seq.genomic.T.hg38 C3N-01024 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/b9c03386-359e-4014-ae3e-f2eeeb30e0b5/9bbc4a91-9fca-458a-8f31-dfd0f0a9009c.rna_seq.genomic.gdc_realn.bam 7103899485 BAM hg38 b9c03386-359e-4014-ae3e-f2eeeb30e0b5 katmai C3N-01024.RNA-Seq.R1.A C3N-01024 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/d3fd7b33-e340-4f70-a6df-b7be7251f916/171215_UNC32-K00270_0073_BHN3NFBBXX_GGCTAC_S9_L003_R1_001.fastq.gz 4130779187 FASTQ NA d3fd7b33-e340-4f70-a6df-b7be7251f916 katmai C3N-01024.RNA-Seq.R1.T C3N-01024 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/565bbf90-d360-4748-93bf-0a41eb61a124/171109_UNC31-K00269_0090_AHLHNWBBXX_ACTTGA_S23_L006_R1_001.fastq.gz 3212271695 FASTQ NA 565bbf90-d360-4748-93bf-0a41eb61a124 katmai C3N-01024.RNA-Seq.R2.A C3N-01024 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/d39ad31f-6a7e-41b0-96c5-93194af85f8a/171215_UNC32-K00270_0073_BHN3NFBBXX_GGCTAC_S9_L003_R2_001.fastq.gz 4809377296 FASTQ NA d39ad31f-6a7e-41b0-96c5-93194af85f8a katmai @@ -9344,7 +9358,9 @@ C3N-02003.MethArray.Red.T C3N-02003 LUAD Methylation Array tumor /diskmnt/Projec C3N-02003.miRNA-Seq.A C3N-02003 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/c28c49f9-fc78-405f-a37d-c1fdf5f91e42/181108_UNC31-K00269_0162_AH255GBBXY_GGTAGC_S48_L004_R1_001.unaln.bam 207987594 BAM NA c28c49f9-fc78-405f-a37d-c1fdf5f91e42 katmai C3N-02003.miRNA-Seq.T C3N-02003 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/47ed4daf-4042-49ee-a2c7-80a43f1bdcb0/181108_UNC31-K00269_0162_AH255GBBXY_ACAGTG_S29_L004_R1_001.unaln.bam 182925682 BAM NA 47ed4daf-4042-49ee-a2c7-80a43f1bdcb0 katmai C3N-02003.RNA-Seq.genomic.A.hg38 C3N-02003 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/77ecaf8b-e278-4e26-9a52-005ab5e4254f/70a16607-35d9-445d-9d36-9b865698787b.rna_seq.genomic.gdc_realn.bam 8296388859 BAM hg38 77ecaf8b-e278-4e26-9a52-005ab5e4254f katmai +C3N-02003.RNA-Seq.genomic.A.hg38 C3N-02003 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/43be6921-b09b-463e-97ea-37810ce9e47e/dd7aaa53-5a9b-4b91-9efd-7250b9d316cf.rna_seq.genomic.gdc_realn.bam 8297119392 BAM hg38 43be6921-b09b-463e-97ea-37810ce9e47e katmai C3N-02003.RNA-Seq.genomic.T.hg38 C3N-02003 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/f2a8fb84-a622-46e3-9776-0785bce9d69a/9bcff1b2-27ff-40a9-94ed-e4cc5b3bc19a.rna_seq.genomic.gdc_realn.bam 6874869311 BAM hg38 f2a8fb84-a622-46e3-9776-0785bce9d69a katmai +C3N-02003.RNA-Seq.genomic.T.hg38 C3N-02003 LUAD RNA-Seq tumor /diskmnt/Projects/cptac/GDC_import/data/7beeeba3-daf0-4a0d-a7bb-49382f4daa99/69fc1ee8-9ba6-4ef8-a5f2-cbe5853bb5e7.rna_seq.genomic.gdc_realn.bam 6876537011 BAM hg38 7beeeba3-daf0-4a0d-a7bb-49382f4daa99 katmai C3N-02003.RNA-Seq.R1.A C3N-02003 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/96a22aec-6a15-4edb-9bf7-027ac1e746e4/180508_UNC31-K00269_0128_BHTY7KBBXX_ATTCCT_S12_L003_R1_001.fastq.gz 3882852681 FASTQ NA 96a22aec-6a15-4edb-9bf7-027ac1e746e4 katmai C3N-02003.RNA-Seq.R1.T C3N-02003 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/ea62e60b-7213-4039-91e0-0e9c733117f2/180508_UNC31-K00269_0128_BHTY7KBBXX_ACAGTG_S7_L007_R1_001.fastq.gz 3160557380 FASTQ NA ea62e60b-7213-4039-91e0-0e9c733117f2 katmai C3N-02003.RNA-Seq.R2.A C3N-02003 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac3_primary_1/GDC_import/data/c99083e8-6f5e-4516-999b-0236384c53e9/180508_UNC31-K00269_0128_BHTY7KBBXX_ATTCCT_S12_L003_R2_001.fastq.gz 4216757340 FASTQ NA c99083e8-6f5e-4516-999b-0236384c53e9 katmai @@ -11383,8 +11399,11 @@ C3N-03073.MethArray.Green.A C3N-03073 LUAD Methylation Array tissue_normal /disk C3N-03073.MethArray.Green.T C3N-03073 LUAD Methylation Array tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/b43577c3-739c-41a7-8a1a-8db170a2c594/203561450114_R04C01_Grn.idat 13676226 IDAT NA b43577c3-739c-41a7-8a1a-8db170a2c594 katmai C3N-03073.MethArray.Red.A C3N-03073 LUAD Methylation Array tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/45625f02-0c51-424b-aadf-7a35681153a0/203561450046_R02C01_Red.idat 13676211 IDAT NA 45625f02-0c51-424b-aadf-7a35681153a0 katmai C3N-03073.MethArray.Red.T C3N-03073 LUAD Methylation Array tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/4fce9541-5697-4617-804d-7ab4b65e093a/203561450114_R04C01_Red.idat 13676226 IDAT NA 4fce9541-5697-4617-804d-7ab4b65e093a katmai +C3N-03073.miRNA-Seq.A C3N-03073 LUAD miRNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/01557f5c-1498-49a7-8ca0-5dcad0b64f33/190722_UNC31-K00269_0234_AH7VGTBBXY_CACCGG_S46_L006_R1_001.unaln.bam 202343629 BAM NA 01557f5c-1498-49a7-8ca0-5dcad0b64f33 katmai C3N-03073.miRNA-Seq.T C3N-03073 LUAD miRNA-Seq tumor /diskmnt/Projects/cptac_downloads_6/GDC_import/data/18b12ad5-0a48-44b0-968f-591fb185fdd2/190722_UNC31-K00269_0234_AH7VGTBBXY_GATCAG_S5_L007_R1_001.unaln.bam 170217266 BAM NA 18b12ad5-0a48-44b0-968f-591fb185fdd2 katmai +C3N-03073.RNA-Seq.R1.A C3N-03073 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/b203accd-ac6f-4096-8b45-578c7365a462/190607_UNC32-K00270_0178_AH773TBBXY_CATAGAGT-TGCCACCA_S20_L005_R1_001.fastq.gz 3911246975 FASTQ NA b203accd-ac6f-4096-8b45-578c7365a462 katmai C3N-03073.RNA-Seq.R1.T C3N-03073 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/9d4ad6ac-66af-4216-8aa2-40531e6b3c32/190612_UNC31-K00269_0223_BH77CWBBXY_TGCGGCGT-CCTCGGTA_S7_L002_R1_001.fastq.gz 4110997799 FASTQ NA 9d4ad6ac-66af-4216-8aa2-40531e6b3c32 katmai +C3N-03073.RNA-Seq.R2.A C3N-03073 LUAD RNA-Seq tissue_normal /diskmnt/Projects/cptac/GDC_import/data/9af1321e-4672-466f-b1b3-8365ead84c06/190607_UNC32-K00270_0178_AH773TBBXY_CATAGAGT-TGCCACCA_S20_L005_R2_001.fastq.gz 4309621063 FASTQ NA 9af1321e-4672-466f-b1b3-8365ead84c06 katmai C3N-03073.RNA-Seq.R2.T C3N-03073 LUAD RNA-Seq tumor /diskmnt/Projects/cptac3_primary_1/GDC_import/data/7a4ecbb4-b7db-4bef-8933-bcee1d84a4d0/190612_UNC31-K00269_0223_BH77CWBBXY_TGCGGCGT-CCTCGGTA_S7_L002_R2_001.fastq.gz 4794736220 FASTQ NA 7a4ecbb4-b7db-4bef-8933-bcee1d84a4d0 katmai C3N-03074.MethArray.Green.A C3N-03074 LUAD Methylation Array tissue_normal /diskmnt/Projects/cptac_downloads_7/GDC_import/data/b35d9e57-b5c0-4699-adc3-c38286a01611/203561450014_R07C01_Grn.idat 13676216 IDAT NA b35d9e57-b5c0-4699-adc3-c38286a01611 katmai C3N-03074.MethArray.Green.T C3N-03074 LUAD Methylation Array tumor /diskmnt/Projects/cptac_downloads_7/GDC_import/data/c8c5b0db-fed6-40c1-a38e-6fc2f0bcb9b8/203561620016_R04C01_Grn.idat 13676221 IDAT NA c8c5b0db-fed6-40c1-a38e-6fc2f0bcb9b8 katmai