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d3b-center / ticket-tracker-OPC

A repo to generate and track tickets for ped OT
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v4 release #22

Closed jharenza closed 3 years ago

jharenza commented 3 years ago

What data file(s) does this issue pertain to?

all files

What release are you using?

v3

Put your question or report your issue here.

For histologies files:

Remove the following files from release: gtex-gene-expression-rsem-tpm-collapsed.polya.rds gtex-histologies.tsv kfnbl-fusion-arriba.tsv.gz kfnbl-fusion-starfusion.tsv.gz kfnbl-gene-counts-rsem-expected_count-collapsed.stranded.rds kfnbl-gene-counts-rsem-expected_count.stranded.rds kfnbl-gene-expression-kallisto.stranded.rds kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds kfnbl-gene-expression-rsem-fpkm.stranded.rds kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds kfnbl-gene-expression-rsem-tpm.stranded.rds kfnbl-histologies.tsv kfnbl-isoform-counts-rsem-expected_count.stranded.rds kfnbl-isoform-expression-rsem-tpm.stranded.rds kfnbl-snv-lancet.vep.maf.gz kfnbl-snv-mutect2.vep.maf.gz kfnbl-snv-strelka2.vep.maf.gz kfnbl-snv-vardict.vep.maf.gz target-histologies.tsv tcga-histologies.tsv

Add generally named files per #24

logstar commented 3 years ago

@jharenza There might be some md5sum mismatches in the v3 release that could be fixed in the v4 release as well.

When downloading the v3 file using the most recent OT/OpenPBTA-analysis download-data.sh, I got the following md5sum mismatches:

Checking MD5 hashes...
gtex-gene-expression-rsem-tpm-collapsed.polya.rds: FAILED
gtex-histologies.tsv: OK
intersect_cds_lancet_strelka_mutect_WGS.bed: FAILED
intersect_strelka_mutect_WGS.bed: OK
kfnbl-fusion-arriba.tsv.gz: OK
kfnbl-fusion-starfusion.tsv.gz: OK
kfnbl-gene-counts-rsem-expected_count.stranded.rds: FAILED
kfnbl-gene-counts-rsem-expected_count-collapsed.stranded.rds: OK
kfnbl-gene-expression-kallisto.stranded.rds: OK
kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds: OK
kfnbl-gene-expression-rsem-fpkm.stranded.rds: FAILED
kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds: OK
kfnbl-gene-expression-rsem-tpm.stranded.rds: FAILED
kfnbl-histologies.tsv: OK
kfnbl-isoform-counts-rsem-expected_count.stranded.rds: OK
kfnbl-isoform-expression-rsem-tpm.stranded.rds: OK
kfnbl-snv-lancet.vep.maf.gz: OK
kfnbl-snv-mutect2.vep.maf.gz: OK
kfnbl-snv-strelka2.vep.maf.gz: OK
kfnbl-snv-vardict.vep.maf.gz: OK
release-notes.md: OK
target-gene-expression-rsem-tpm-collapsed.rds: FAILED
target-histologies.tsv: OK
tcga-gene-expression-rsem-tpm-collapsed.rds: FAILED
tcga-histologies.tsv: OK
WGS.hg38.lancet.300bp_padded.bed: OK
WGS.hg38.lancet.unpadded.bed: OK
WGS.hg38.mutect2.vardict.unpadded.bed: OK
WGS.hg38.strelka2.unpadded.bed: OK
WGS.hg38.vardict.100bp_padded.bed: OK
md5sum: WARNING: 7 computed checksums did NOT match

For example, the md5sum of the dowloaded target-gene-expression-rsem-tpm-collapsed.rds is 4ea6cb1a65e5c9698b07b7408529d308, whereas the md5sum in v3 release md5sum.txt is 1a2444fde3b488168e0d3958a2d1b937.

I re-downloaded the v3 release and got the same md5sum mismatches.

readRDS in the docker RStudio gives the following error:

> readRDS('data/v3/gtex-gene-expression-rsem-tpm-collapsed.polya.rds')
Error in readRDS("data/v3/gtex-gene-expression-rsem-tpm-collapsed.polya.rds") : 
  unknown input format
jharenza commented 3 years ago

@logstar can you delete those files and try to run the download script again? sometimes if they download partially and give a mismatch, you need to delete so they can re-download. let me know!

jharenza commented 3 years ago

my release file for target-gene-expression-rsem-tpm-collapsed.rds matches that in the release md5sum.txt harenzaj@38f9d38f36c9 v3 % md5sum target-gene-expression-rsem-tpm-collapsed.rds 1a2444fde3b488168e0d3958a2d1b937 target-gene-expression-rsem-tpm-collapsed.rds

logstar commented 3 years ago

@logstar can you delete those files and try to run the download script again? sometimes if they download partially and give a mismatch, you need to delete so they can re-download. let me know!

my release file for target-gene-expression-rsem-tpm-collapsed.rds matches that in the release md5sum.txt harenzaj@38f9d38f36c9 v3 % md5sum target-gene-expression-rsem-tpm-collapsed.rds 1a2444fde3b488168e0d3958a2d1b937 target-gene-expression-rsem-tpm-collapsed.rds

I deleted target-gene-expression-rsem-tpm-collapsed.rds and rerun bash download-data.sh, but the md5sum still mismatches.

I think the md5sum mismatched files are not available at https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3 . For example, https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3/target-gene-expression-rsem-tpm-collapsed.rds links to an error saying the "The specified key does not exist".

The matched files are available. For example, https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3/tcga-histologies.tsv links to a file for downloading, and its md5sum matches v3 release md5sum.txt.

jharenza commented 3 years ago

Also adding to this that we need to add count matrices for GTEX, TARGET, and TCGA per #27

logstar commented 3 years ago

Also adding to this that we need to add count matrices for GTEX, TARGET, and TCGA per #27

Thank you for the note.

target-gene-expression-rsem-tpm-collapsed.rds is available at https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3/target-gene-expression-rsem-tpm-collapsed.rds now, and its md5sum matches v3 release md5sum.txt.

The following files are still not available, as their URLs still link to error messages.

jharenza commented 3 years ago

@logstar can you delete those files and try to run the download script again? sometimes if they download partially and give a mismatch, you need to delete so they can re-download. let me know!

my release file for target-gene-expression-rsem-tpm-collapsed.rds matches that in the release md5sum.txt harenzaj@38f9d38f36c9 v3 % md5sum target-gene-expression-rsem-tpm-collapsed.rds 1a2444fde3b488168e0d3958a2d1b937 target-gene-expression-rsem-tpm-collapsed.rds

I deleted target-gene-expression-rsem-tpm-collapsed.rds and rerun bash download-data.sh, but the md5sum still mismatches.

I think the md5sum mismatched files are not available at https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3 . For example, https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3/target-gene-expression-rsem-tpm-collapsed.rds links to an error saying the "The specified key does not exist".

The matched files are available. For example, https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/open-targets/v3/tcga-histologies.tsv links to a file for downloading, and its md5sum matches v3 release md5sum.txt.

ok, it looks like these may have deleted, but i just put them back - can you try again?

logstar commented 3 years ago

@jharenza Thank you for the quick reply.

All files are available now, and their md5sums all match v3 release md5sum.txt.

jharenza commented 3 years ago

Great!

jharenza commented 3 years ago

closed with https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/16

logstar commented 3 years ago

Hi @jharenza . Thank you for preparing the v4 release.

I was wondering which column of the v4/histologies.tsv matches the column names of v4/gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds.

Following are the last 10 rows of v4/histologies.tsv:

Kids_First_Biospecimen_ID sample_id aliquot_id Kids_First_Participant_ID experimental_strategy sample_type composition tumor_descriptor primary_site age_bracket reported_gender race ethnicity diagnosis_type diagnosis_category age_at_diagnosis_days pathology_diagnosis RNA_library EFS_days OS_days OS_status PFS_days cohort age_last_update_days seq_center parent_aliquot_id previous_parent_aliquot_id cancer_predispositions previous_cancer_predispositions pathology_free_text_diagnosis cohort_participant_id germline_sex_estimate extent_of_tumor_resection normal_fraction tumor_fraction tumor_ploidy CNS_region molecular_subtype integrated_diagnosis Notes harmonized_diagnosis broad_histology short_histology cancer_group gtex_group gtex_subgroup
GTEX-15UF6-1426-SM-AIGJD AIGJD NA 15UF6 RNA-Seq Normal Solid Tissue NA Spleen NA Female NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-15UF6 NA NA NA NA NA NA NA NA 2 pieces moderate congestion fragmented tissue NA NA NA NA Spleen Spleen
GTEX-11PRG-0426-SM-4XJA1 4XJA1 NA 11PRG RNA-Seq Normal Solid Tissue NA Testis NA Male NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-11PRG NA NA NA NA NA NA NA NA "2 pieces moderately autolyzed spermatogenesis is present" NA NA NA NA Testis Testis
GTEX-1LGRB-2626-SM-B4CPO B4CPO NA 1LGRB RNA-Seq Normal Solid Tissue NA Muscle - Skeletal NA Female NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-1LGRB NA NA NA NA NA NA NA NA "2 pieces skeletal muscle with small portion of attached and internal fat scattered fibers with degenerative change" NA NA NA NA Muscle Muscle - Skeletal
GTEX-ZT9X-0626-SM-4UJTS 4UJTS NA ZT9X RNA-Seq Normal Solid Tissue NA Esophagus - Muscularis NA Male NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-ZT9X NA NA NA NA NA NA NA NA "5 pieces all muscularis" NA NA NA NA Esophagus Esophagus - Muscularis
GTEX-XOTO-1926-SM-42ZNC 42ZNC NA XOTO RNA-Seq Normal Solid Tissue NA Artery - Coronary NA Male NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-XOTO NA NA NA NA NA NA NA NA 2 pieces. 2x2 &amp 2x2mm calcified (delineated) atherosclerosis with ~60% occlusion NA NA NA NA Artery Artery - Coronary
GTEX-13O21-1026-SM-59K21 59K21 NA 13O21 RNA-Seq Normal Solid Tissue NA Small Intestine - Terminal Ileum NA Male NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-13O21 NA NA NA NA NA NA NA NA "6 pieces 10% lymphoid aggregates delineated best for LCM or TMA studies" NA NA NA NA Small Intestine Small Intestine - Terminal Ileum
GTEX-W5X1-2926-SM-3C8J7 3C8J7 NA W5X1 RNA-Seq Normal Solid Tissue NA Artery - Tibial NA Female NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-W5X1 NA NA NA NA NA NA NA NA "2 pieces 5x1 &amp 5x3.5mm heavily calcified half of 1 piece without lesion" NA NA NA NA Artery Artery - Tibial
GTEX-WFG7-1226-SM-3BRN1 3BRN1 NA WFG7 RNA-Seq Normal Solid Tissue NA Esophagus - Gastroesophageal Junction NA Male NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-WFG7 NA NA NA NA NA NA NA NA "6 pieces ~8x4mm. All muscle no mucosa excellent specimens" NA NA NA NA Esophagus Esophagus - Gastroesophageal Junction
GTEX-XV7Q-2726-SM-7LDFM 7LDFM NA XV7Q RNA-Seq Normal Solid Tissue NA Nerve - Tibial NA Female NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-XV7Q NA NA NA NA NA NA NA NA "2 pieces 7.5x5 &amp 8x6mm ~1-15.mm rim of discontinuous flat rep areas delineated" NA NA NA NA Nerve Nerve - Tibial
GTEX-ZDTS-0826-SM-4S8WD 4S8WD NA ZDTS RNA-Seq Normal Solid Tissue NA Skin - Not Sun Exposed (Suprapubic) NA Male NA NA NA NA NA NA poly-A NA NA DECEASED NA GTEx NA Broad Institute of MIT and Harvard NA NA NA NA NA GTEX-ZDTS NA NA NA NA NA NA NA NA 6 pieces many hair follicles (avoid pubic hair) well trimmed of subcutaneous fat NA NA NA NA Skin Skin - Not Sun Exposed (Suprapubic)

Following are typical column names of v4/gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds:

1   SRR1068687
2   SRR1068788
3   SRR1068808
4   SRR1068832
5   SRR1068855
6   SRR1068880
7   SRR1068905
8   SRR1068929
9   SRR1068953
10  SRR1068977
11  SRR1068999
...
8361    b2cb10b8-0554-4ffa-ace1-b00f83c2fa0f
8362    b31102b7-d51b-423d-aa5f-7ca3404dc5c0
8363    b3301ee7-7b60-44a0-b03f-64e01b56d873
8364    b39c65c2-a792-4933-888f-2b4f58140808
8365    b3aa1087-e311-48c3-9739-f78164639f05
8366    b3fdff01-8c52-4947-a117-d79170ec4309
...
19889   ffe5563c-6b36-4ad9-a61e-127b6c053727
19890   fff736ee-ac9b-4bfb-87f0-03cd8e940e9e
19891   fffd244f-bd0f-4d09-8ab3-43bc0b20e297

I also cannot find SRR1068687 in the whole v4/histologies.tsv.

This matching is relevant to the histology z-score analysis and NBL vs GTEX stably expressed gene analysis.

jharenza commented 3 years ago

@logstar thanks for finding this issue. I just filed #31 for this - will see if @ewafula or @komalsrathi has a mapping file you can use temporarily. Sorry about that!

logstar commented 3 years ago

@logstar thanks for finding this issue. I just filed #31 for this - will see if @ewafula or @komalsrathi has a mapping file you can use temporarily. Sorry about that!

@jharenza Thank you for the quick reply. No worries at all. I can imagine the complexity of integrate multiple datasets together. Also, I can use dummy data to work on the analysis procedures before the real data become available.

komalsrathi commented 3 years ago

Interesting - the file that I had uploaded i.e. gtex-histologies.tsv should have this sample:

grep SRR1068687 ~/Projects/PediatricOpenTargets/OpenPBTA-analysis/analyses/rnaseq-batch-correct/input/gtex-histologies.tsv 

54  unavailable unavailable Normals GTEX-XXEK   dead    GTEX-XXEK-0526-SM-4BRWD male    Esophagus   Esophagus - Gastroesophageal Junction   poly-A  SRR1068687  GTEx
komalsrathi commented 3 years ago

Oh but you need a mapping file - let me check!

komalsrathi commented 3 years ago

gtex_mapping.txt @logstar I have this - let me know if this does not work for you.

komalsrathi commented 3 years ago

And just in case!

tcga_mapping.txt target_mapping.txt

cc: @jharenza

sangeetashukla commented 3 years ago

@komalsrathi @jharenza Perfect, I needed the same files, Thank you.

logstar commented 3 years ago

@komalsrathi Thank you for the quick reply. The mapping files work for me.

jharenza commented 3 years ago

thanks @komalsrathi !

jharenza commented 3 years ago

Interesting - the file that I had uploaded i.e. gtex-histologies.tsv should have this sample:

grep SRR1068687 ~/Projects/PediatricOpenTargets/OpenPBTA-analysis/analyses/rnaseq-batch-correct/input/gtex-histologies.tsv 

54    unavailable unavailable Normals GTEX-XXEK   dead    GTEX-XXEK-0526-SM-4BRWD male    Esophagus   Esophagus - Gastroesophageal Junction   poly-A  SRR1068687  GTEx

ahh, we updated to all 17k samples for re-processing, which did not include SRR from their portal.

ewafula commented 3 years ago

thanks @komalsrathi! @jharenza, do we need to have an additional column in the histologies.txt file with sample ids used in the expression RDS files such as SRR*?

jharenza commented 3 years ago

@ewafula no, we will update the RSEM files to your IDs

logstar commented 3 years ago

Thank you again for the mapping files. @komalsrathi

I found some TCGA sample_barcodes are mapped to multiple sample_ids, and some of their expected count sums are different in gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds, as shown in the following table.

@jharenza I was wondering if these duplicates will be resolved in the future releases. For now, I will only keep one of the samples that have the same rsem_expected_cnt_colSums.

sample_barcode sample_id rsem_expected_cnt_colSum
TCGA-37-4132-01A-01R-1100-07 44d729b9-be8f-4ae3-ae4d-b71c9d8463f4 59037096.86
TCGA-37-4132-01A-01R-1100-07 f3f5bd65-72fc-4cee-befb-2b6446be005e 59037096.86
TCGA-37-4133-01A-01R-1100-07 4f8ed570-458a-45c5-ad5c-c254812a4b40 63576672.73
TCGA-37-4133-01A-01R-1100-07 ecb95d43-cada-4159-aeca-197dccd8fcfd 63576672.73
TCGA-38-4625-01A-01R-1206-07 619f167f-d0c0-468f-b6d1-801bf6c0b017 82024039.49
TCGA-38-4625-01A-01R-1206-07 d73deb65-5df1-4fee-bcc6-56b301d77595 39274.99
TCGA-A2-A0EM-01A-11R-A034-07 2aaed860-0ed5-4c5e-9842-60aa13785b58 62357901.34
TCGA-A2-A0EM-01A-11R-A034-07 c90db6f3-03b4-4092-8efb-4925a423130d 62357901.34
TCGA-A6-2672-01B-03R-2302-07 d32d94d4-0b92-4dc1-b3e9-750071f2d7e0 21980139.14
TCGA-A6-2672-01B-03R-2302-07 f489a86d-ab77-442c-a89d-ee734faf9caf 23162032.49
TCGA-A6-5661-01B-05R-2302-07 298bf211-99f7-44dd-802e-3f1aa3682681 7300714.54
TCGA-A6-5661-01B-05R-2302-07 bfb2cdbd-42f2-4784-9450-81236eb39c85 37621239.56
TCGA-A6-5665-01B-03R-2302-07 373b0a02-88d2-49fb-8580-e9933a35c7b8 17227691.85
TCGA-A6-5665-01B-03R-2302-07 bdf3b4b3-1619-4ced-8e73-ebde54838291 29470181.82
TCGA-A7-A0DC-01A-11R-A00Z-07 1b000b10-0b4c-4b56-bfb6-950889775865 108936872.87
TCGA-A7-A0DC-01A-11R-A00Z-07 5748a77b-0ea0-487b-982f-ccc2f8bab563 72140078.13
TCGA-A7-A0DC-01A-11R-A00Z-07 98a04bbb-0a89-4809-ad5b-9289a0cdf517 72140078.13
TCGA-A7-A0DC-01B-04R-A22O-07 4b66df1d-9408-4e25-aaf7-2825809baa0c 48575580.67
TCGA-A7-A0DC-01B-04R-A22O-07 b043709e-acfb-4034-838e-768c894f54dc 31444946.25
TCGA-A7-A0DC-01B-04R-A22O-07 e59455b1-4bfa-45c2-be8a-1cd8f3a26c0e 25507397.89
TCGA-A7-A0DC-11A-41R-A089-07 9ba3e93f-6b7f-464b-9012-7e26592216d3 50908011.83
TCGA-A7-A0DC-11A-41R-A089-07 e90e4988-b2fb-4aa0-864e-84320abba5c0 50908011.83
TCGA-A7-A13G-01A-11R-A13Q-07 8e41a6eb-590f-4c75-ba43-33883f6402bb 80857822.17
TCGA-A7-A13G-01A-11R-A13Q-07 9e8d6775-5f94-4a53-aed6-08a18b33a701 111945370.88
TCGA-A7-A13G-01B-04R-A22O-07 5195e2af-0a23-40e3-a13c-69ea0b306287 27946848.41
TCGA-A7-A13G-01B-04R-A22O-07 9612e42a-5464-4b48-b7df-819a791bf598 50825075.61
TCGA-A7-A13G-01B-04R-A22O-07 b80cbb60-df1a-4b4a-bf1b-0b1a04e64078 21767339.23
TCGA-A7-A26F-01A-21R-A169-07 0aa1751e-1661-4b8b-9e5a-cc7edf6f8a8c 98378280.28
TCGA-A7-A26F-01A-21R-A169-07 3d2a9024-b722-4092-989e-bbc1d1332be9 125851647.25
TCGA-A7-A26F-01B-04R-A22O-07 0c30f5b1-5ed5-48d1-b8df-df4611761dd3 52560800.24
TCGA-A7-A26F-01B-04R-A22O-07 822d3bb2-b845-4073-a5fb-7ecf9e5c10a1 23021884.5
TCGA-A7-A26F-01B-04R-A22O-07 d7f11b34-6b38-4a7a-80b1-fae9b7243caf 27747876.78
TCGA-A7-A26I-01A-11R-A169-07 0752afb5-f92b-4a55-921c-2f36674e8689 82498866.41
TCGA-A7-A26I-01A-11R-A169-07 2c8cb5e5-dd58-47f1-9d4e-bdf7559efc6e 140091800.87
TCGA-A7-A26I-01B-06R-A22O-07 373504b8-416a-4bae-9e62-ebf13d22a337 58832935.61
TCGA-A7-A26I-01B-06R-A22O-07 a965f4a8-076e-460e-91bb-f821711a63e5 11715966.18
TCGA-A7-A26I-01B-06R-A22O-07 f7e4051b-a5f1-4be0-b139-43e5ef75644e 29322709.95
TCGA-AC-A2QH-01A-11R-A18M-07 8fe05303-7df7-48a3-862c-e17b39a670c2 30632024.4
TCGA-AC-A2QH-01A-11R-A18M-07 b334f93f-48ff-434a-b6bc-8bc0920a5ce8 132806590.93
TCGA-AC-A2QH-01B-04R-A22O-07 6c008c2f-bcc4-4497-962e-8e76879b3ecb 55621677.64
TCGA-AC-A2QH-01B-04R-A22O-07 75c3e5e4-ef05-467f-9e7e-d3003db187b1 35090851.18
TCGA-AC-A2QH-01B-04R-A22O-07 7de0e920-e411-4994-a6d8-460cfcef9bdd 22928152.09
TCGA-AC-A3OD-01A-11R-A21T-07 e9de5496-4486-4ceb-b3b3-30a53b2c52f6 105998355.69
TCGA-AC-A3OD-01A-11R-A21T-07 e9f7caba-a833-4c3c-82f2-11d7a233974d 112332806.62
TCGA-AC-A3OD-01B-06R-A22O-07 84a6ed5e-ad73-4399-ac37-381721f3b4e8 32717482.06
TCGA-AC-A3OD-01B-06R-A22O-07 99ce385c-e0e2-41c2-a868-40a31eac1e50 49766248.16
TCGA-AC-A3OD-01B-06R-A22O-07 a03f6b87-d762-479a-9132-aa42563bacc4 90946986.92999999
TCGA-AC-A3QQ-01A-11R-A22K-07 32911f1f-0202-4bb2-be86-4b68e5afcc00 125602035.27
TCGA-AC-A3QQ-01A-11R-A22K-07 81d1e125-7e15-4563-87c0-b0bfa9dfcad7 52836757.19
TCGA-AC-A3QQ-01B-06R-A22O-07 7af8074e-e82b-4e9e-a66c-3bb0097e1a5b 30938541.95
TCGA-AC-A3QQ-01B-06R-A22O-07 7d9d1e8c-710d-4b17-a3cd-8cd6208d3c08 13001988.01
TCGA-AK-3425-01A-02R-1277-07 211b37ea-f8ba-4023-b622-15d3e2543505 38348466.47
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jharenza commented 3 years ago

@logstar would you mind adding this info to a new issue since this issue is closed? Thank you!

logstar commented 3 years ago

@logstar would you mind adding this info to a new issue since this issue is closed? Thank you!

Sure. I will create a new issue with this info.