From 1b509593757902d57d5bb206d592cbf8f37d37b9 Mon Sep 17 00:00:00 2001
From: Tianyu Lan <tianyu.lan@hhu.de>
Date: Mon, 22 Jul 2024 15:36:38 +0200
Subject: [PATCH] First data upload leaf_RNA_quant

---
 .gitattributes                                |  41 +++----
 .gitignore                                    | 112 +++++++++---------
 assays/RNAseq_analysis_of_leaf/README.md      |  12 +-
 .../AT113_quant/aux_info/ambig_info.tsv       |   3 +
 .../AT113_quant/aux_info/expected_bias.gz     |   3 +
 .../AT113_quant/aux_info/fld.gz               |   3 +
 .../AT113_quant/aux_info/meta_info.json       |   3 +
 .../AT113_quant/aux_info/observed_bias.gz     |   3 +
 .../AT113_quant/aux_info/observed_bias_3p.gz  |   3 +
 .../leaf_RNA_quant/AT113_quant/cmd_info.json  |   3 +
 .../AT113_quant/libParams/flenDist.txt        |   3 +
 .../AT113_quant/lib_format_counts.json        |   3 +
 .../AT113_quant/logs/salmon_quant.log         |   3 +
 .../leaf_RNA_quant/AT113_quant/quant.sf       |   3 +
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 .../AT114_quant/aux_info/expected_bias.gz     |   3 +
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 .../AT116_quant/aux_info/observed_bias.gz     |   3 +
 .../AT116_quant/aux_info/observed_bias_3p.gz  |   3 +
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+# taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+# Icon must end with two \r
+Icon
+# Thumbnails
+._*
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
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+.Trashes
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+.AppleDB
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+Temporary Items
+.apdisk
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+# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+# Dump file
+*.stackdump
+# Folder config file
+[Dd]esktop.ini
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+# Windows shortcuts
+*.lnk
+# ----- linux rules -----
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+*~
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diff --git a/assays/RNAseq_analysis_of_leaf/README.md b/assays/RNAseq_analysis_of_leaf/README.md
index 4aa060d..cbf7623 100644
--- a/assays/RNAseq_analysis_of_leaf/README.md
+++ b/assays/RNAseq_analysis_of_leaf/README.md
@@ -1,6 +1,6 @@
-RNAseq analysis was conducted on the leaf and main shoot apex (MSA) samples separately.
-
-The tables of Count and Transcript per Million (TPM) were obtained using ThreeDRNAseq R package.
-The tables of differentially expressed genes were obtained using EdgeR R package.
-Gene Ontology analysis was performed using the Triticeae-Gene Tribe database (http://wheat.cau.edu.cn/TGT/m15/?navbar=GOEnrichment).
-WCGNA analysis was performed using the WGCNA R package.
+RNAseq analysis was conducted on the leaf and main shoot apex (MSA) samples separately.
+
+The tables of Count and Transcript per Million (TPM) were obtained using ThreeDRNAseq R package.
+The tables of differentially expressed genes were obtained using EdgeR R package.
+Gene Ontology analysis was performed using the Triticeae-Gene Tribe database (http://wheat.cau.edu.cn/TGT/m15/?navbar=GOEnrichment).
+WCGNA analysis was performed using the WGCNA R package.
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new file mode 100644
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--- /dev/null
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diff --git a/assays/Salmon_quantification/protocols/salmon_indexing.bash b/assays/Salmon_quantification/protocols/salmon_indexing.bash
index 28b510a..70a15e7 100644
--- a/assays/Salmon_quantification/protocols/salmon_indexing.bash
+++ b/assays/Salmon_quantification/protocols/salmon_indexing.bash
@@ -1,7 +1,7 @@
-### Load module
-
-module load Salmon/1.6.0
-
-### Script command
-salmon index -t BaRT.1.0_Unsplit_exons_padded.fasta -i BaRT.1.0_Unsplit_exons_padded.fasta_index
-
+### Load module
+
+module load Salmon/1.6.0
+
+### Script command
+salmon index -t BaRT.1.0_Unsplit_exons_padded.fasta -i BaRT.1.0_Unsplit_exons_padded.fasta_index
+
diff --git a/assays/Salmon_quantification/protocols/salmon_quantification.bash b/assays/Salmon_quantification/protocols/salmon_quantification.bash
index a3e742a..77cb108 100644
--- a/assays/Salmon_quantification/protocols/salmon_quantification.bash
+++ b/assays/Salmon_quantification/protocols/salmon_quantification.bash
@@ -1,8 +1,8 @@
-### Load module
-
-module load Salmon/1.6.0
-
-### Script command
-
-salmon quant -i BaRT.1.0_Unsplit_exons_padded.fasta_index -l A -1 sample_*_1.fq.gz -2 sample_*_2.fq.gz -p 4 --validateMappings -o sample_quant
-
+### Load module
+
+module load Salmon/1.6.0
+
+### Script command
+
+salmon quant -i BaRT.1.0_Unsplit_exons_padded.fasta_index -l A -1 sample_*_1.fq.gz -2 sample_*_2.fq.gz -p 4 --validateMappings -o sample_quant
+
-- 
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