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end with two \r -Icon -# Thumbnails -._* -# Files that might appear in the root of a volume -.DocumentRevisions-V100 -.fseventsd -.Spotlight-V100 -.TemporaryItems -.Trashes -.VolumeIcon.icns -.com.apple.timemachine.donotpresent -# Directories potentially created on remote AFP share -.AppleDB -.AppleDesktop -Network Trash Folder -Temporary Items -.apdisk -# ----- windows rules ----- -# 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 -$RECYCLE.BIN/ -# Windows Installer files -*.cab -*.msi -*.msix -*.msm -*.msp -# Windows shortcuts -*.lnk -# ----- linux rules ----- -# taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore -*~ -# temporary files which can be created if a process still has a handle open of a deleted file -.fuse_hidden* -# KDE directory preferences -.directory -# Linux trash folder which might appear on any partition or disk -.Trash-* -# .nfs files are created when an open file is removed but is still being accessed -.nfs* +# ----- macos rules ----- +# taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore +# General +.DS_Store +.AppleDouble +.LSOverride +# Icon must end with two \r +Icon +# Thumbnails +._* +# Files that might appear in the root of a volume +.DocumentRevisions-V100 +.fseventsd +.Spotlight-V100 +.TemporaryItems +.Trashes +.VolumeIcon.icns +.com.apple.timemachine.donotpresent +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk +# ----- windows rules ----- +# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore +# Windows thumbnail cache files +Thumbs.db +Thumbs.db:encryptable +ehthumbs.db +ehthumbs_vista.db +# Dump file +*.stackdump +# Folder config file +[Dd]esktop.ini +# Recycle Bin used on file shares +$RECYCLE.BIN/ +# Windows Installer files +*.cab +*.msi +*.msix +*.msm +*.msp +# Windows shortcuts +*.lnk +# ----- linux rules ----- +# taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore +*~ +# temporary files which can be created if a process still has a handle open of a deleted file +.fuse_hidden* +# KDE directory preferences +.directory +# Linux trash folder which might appear on any partition or disk +.Trash-* +# .nfs files are created when an open file is removed but is still being accessed +.nfs* diff --git a/assays/RNAseq_analysis_of_leaf/README.md b/assays/RNAseq_analysis_of_leaf/README.md index 4aa060d925a359e3a43f0d5c70eee252684cf17a..cbf762352c6bbe819864f42a1a0ec2cb2111535e 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. diff --git a/assays/Salmon_quantification/dataset/leaf_RNA_quant/AT113_quant/aux_info/ambig_info.tsv 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+oid sha256:59684afda8858ff01ac97fcb0730d8425a2cbb1b3425a73d6da4747466d757cb +size 4006 diff --git a/assays/Salmon_quantification/dataset/leaf_RNA_quant/tl_9_quant/quant.sf b/assays/Salmon_quantification/dataset/leaf_RNA_quant/tl_9_quant/quant.sf new file mode 100644 index 0000000000000000000000000000000000000000..ce7e191749c88927132c54c3926079dcc1ef9820 --- /dev/null +++ b/assays/Salmon_quantification/dataset/leaf_RNA_quant/tl_9_quant/quant.sf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c618b7549151701b265b3f3edbec372bb99c8a0c47565ff5c34bc1ed13728a41 +size 8494173 diff --git a/assays/Salmon_quantification/protocols/salmon_indexing.bash b/assays/Salmon_quantification/protocols/salmon_indexing.bash index 28b510aa46f4973fefbf5d8ac8c377c69cd4d4c1..70a15e79b432ef80bd9a487e8bfdd343e9a38118 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 a3e742afd1c83cbd481fd3709e1ada79928af61f..77cb10808d788ca303edafbeb29eaa89984b13b8 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 +