From f87b17375f41d9343a954a416697c4ed374191ac Mon Sep 17 00:00:00 2001
From: Dominik <dominik.brilhaus@hhu.de>
Date: Thu, 20 Apr 2023 18:47:16 +0200
Subject: [PATCH] polish file trees
---
assays/Brilhaus2015_PE_mRNASeq/README.md | 8 +++++++-
assays/Brilhaus2015_SE_mRNASeq/README.md | 8 +++++++-
assays/Maleckova2018_aba_mRNASeq/README.md | 6 ++++--
assays/Maleckova2019_A_Oxford_Nanopore/README.md | 4 ++--
assays/Maleckova2019_B_Illumina_HiSeq_DNASeq/README.md | 4 ++--
assays/Maleckova2019_C_PacBio_Isoseq/README.md | 4 ++--
6 files changed, 24 insertions(+), 10 deletions(-)
diff --git a/assays/Brilhaus2015_PE_mRNASeq/README.md b/assays/Brilhaus2015_PE_mRNASeq/README.md
index 171c13a2d..d8090d33f 100644
--- a/assays/Brilhaus2015_PE_mRNASeq/README.md
+++ b/assays/Brilhaus2015_PE_mRNASeq/README.md
@@ -1,4 +1,9 @@
-../hhu_talinum_genome/assays/Brilhaus2015_PE_mRNASeq/dataset/
+# Brilhaus2015_PE_mRNASeq
+
+:bulb: Data files listed here are not yet available via git
+
+```bash
+./dataset/
├── [790M] DB_173_reC3_ED_GAGTGG_L001_R1_001.fastq.gz
├── [781M] DB_173_reC3_ED_GAGTGG_L001_R2_001.fastq.gz
├── [1016M] DB_201_reC3_EN_CGATGT_L001_R1_001.fastq.gz
@@ -13,3 +18,4 @@
└── [907M] DB_77_CAM_MN_GCCAAT_L001_R2_001.fastq.gz
10G used in 0 directories, 12 files
+```
\ No newline at end of file
diff --git a/assays/Brilhaus2015_SE_mRNASeq/README.md b/assays/Brilhaus2015_SE_mRNASeq/README.md
index 8d58efada..c4dad2323 100644
--- a/assays/Brilhaus2015_SE_mRNASeq/README.md
+++ b/assays/Brilhaus2015_SE_mRNASeq/README.md
@@ -1,4 +1,9 @@
-../hhu_talinum_genome/assays/Brilhaus2015_SE_mRNASeq/dataset/
+# Brilhaus2015_SE_mRNASeq
+
+:bulb: Data files listed here are not yet available via git
+
+```bash
+./dataset/
├── [1.6G] DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
├── [1.8G] DB_111_CAMED_ACAGTG_L002_R1_001.fastq.gz
├── [1.9G] DB_113_CAMED_GCCAAT_L002_R1_001.fastq.gz
@@ -25,3 +30,4 @@
└── [1.8G] DB_99_CAMMD_CTTGTA_L001_R1_001.fastq.gz
40G used in 0 directories, 24 files
+```
\ No newline at end of file
diff --git a/assays/Maleckova2018_aba_mRNASeq/README.md b/assays/Maleckova2018_aba_mRNASeq/README.md
index 579592cf1..79f001291 100644
--- a/assays/Maleckova2018_aba_mRNASeq/README.md
+++ b/assays/Maleckova2018_aba_mRNASeq/README.md
@@ -1,8 +1,9 @@
# Maleckova2018_aba_mRNASeq
-## Accession numbers
+:bulb: Data files listed here are not yet available via git
-The read data as well as processed files are deposited at the National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE116590 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116590).../hhu_talinum_genome/assays/Maleckova2018_aba_mRNASeq/dataset/
+```bash
+./dataset/
├── [2.2G] 311_S73_L007_R1_001.fastq.gz
├── [2.0G] 312_S74_L007_R1_001.fastq.gz
├── [2.3G] 313_S75_L007_R1_001.fastq.gz
@@ -29,3 +30,4 @@ The read data as well as processed files are deposited at the Nation
└── [1.9G] 334_S96_L008_R1_001.fastq.gz
50G used in 0 directories, 24 files
+```
\ No newline at end of file
diff --git a/assays/Maleckova2019_A_Oxford_Nanopore/README.md b/assays/Maleckova2019_A_Oxford_Nanopore/README.md
index 6e4c399f9..ae93666c0 100644
--- a/assays/Maleckova2019_A_Oxford_Nanopore/README.md
+++ b/assays/Maleckova2019_A_Oxford_Nanopore/README.md
@@ -1,9 +1,9 @@
# Maleckova2019_A_Oxford_Nanopore
-:bulb: Data files listed here are not yet available via git due to LFS issues (March 14 2023)
+:bulb: Data files listed here are not yet available via git
```bash
-assays/Maleckova2019_A_Oxford_Nanopore/dataset/
+./dataset/
├── [112G] 261-NGS-041019-0
│  ├── [ 31G] Talinum1.zip
│  ├── [ 25G] Talinum2.zip
diff --git a/assays/Maleckova2019_B_Illumina_HiSeq_DNASeq/README.md b/assays/Maleckova2019_B_Illumina_HiSeq_DNASeq/README.md
index e3d129d71..ae480cccd 100644
--- a/assays/Maleckova2019_B_Illumina_HiSeq_DNASeq/README.md
+++ b/assays/Maleckova2019_B_Illumina_HiSeq_DNASeq/README.md
@@ -1,9 +1,9 @@
# Maleckova2019_B_Illumina_HiSeq_DNASeq
-:bulb: Data files listed here are not yet available via git due to LFS issues (March 14 2023)
+:bulb: Data files listed here are not yet available via git
```bash
-assays/Maleckova2019_B_Illumina_HiSeq_DNASeq/dataset/
+./dataset/
├── [692K] 14-7_S1_L008_R1_001_fastqc.html
├── [423K] 14-7_S1_L008_R1_001_fastqc.zip
├── [ 25G] 14-7_S1_L008_R1_001.fastq.gz
diff --git a/assays/Maleckova2019_C_PacBio_Isoseq/README.md b/assays/Maleckova2019_C_PacBio_Isoseq/README.md
index 17543c0d8..493a2d705 100644
--- a/assays/Maleckova2019_C_PacBio_Isoseq/README.md
+++ b/assays/Maleckova2019_C_PacBio_Isoseq/README.md
@@ -1,10 +1,10 @@
# Maleckova2019_C_PacBio_Isoseq
-:bulb: Data files listed here are not yet available via git due to LFS issues (March 14 2023)
+:bulb: Data files listed here are not yet available via git
```bash
-assays/Maleckova2019_C_PacBio_Isoseq/dataset/
+./dataset/
└── [698G] 160-NGS-050619_IsoSeq-TT
├── [196G] Cell1
│  └── [196G] 1_D06
--
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