modify

.gitattributes

@@ -14,3 +14,7 @@ assays/RNAseq/dataset/m_12/m_12_1.fq.gz filter=lfs diff=lfs merge=lfs -text
 assays/RNAseq/dataset/m_17/m_17_2.fq.gz filter=lfs diff=lfs merge=lfs -text
 assays/RNAseq/dataset/m_18/m_18_2.fq.gz filter=lfs diff=lfs merge=lfs -text
 assays/RNAseq/dataset/m_19/m_19_1.fq.gz filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_transcripts_leaf.csv filter=lfs diff=lfs merge=lfs -text

assays/RNAseq_analysis_of_leaf/README.md

+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.

assays/Salmon_quantification/protocols/salmon_indexing.bash

+### 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
+

assays/Salmon_quantification/protocols/salmon_quantification.bash

+### 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
+