README.md

Analysis of smallRNA-seq data obtained from Blumeria graminis f.sp. hordei-infected barley

In this repository, we summarize the scripts and pipelines used to perform the analysis of smallRNA-seq data obtained from Blumeria graminis f.sp. hordei-infected barley. The publication can be found here.

Index

1. Raw sequencing data processing.
2. Read length distribution analysis.
3. RFAM BLAST analysis of reads.
4. ShortStack analyis for milRNA discovery in H. vulgare and B. graminis f.sp. hordei
5. NMDS, PCC, and PCA.
6. Co-expression network analysis by WGCNA
7. Differential expression analysis of milRNAs in H. vulgare and B. graminis f.sp. hordei
8. Gene Ontology (GO) enrichment

References

• ShortStack Publication
• Trimmomatic Publication | Manual
• MMSeqs2 Publication | Manual/Repository
• featureCounts Publication
• Samtools Publication | Manual
• BEDtools Publication | Manual
• gffread Manual
• SeqKit Publication | Manual
• BBmap Manual
• NCBI Blast+ Website
• RepeatMasker Website
• DESeq2 Publication | Manual
• EdgeR Publication | Manual
• Limma-VOOM Publication | Manual
• WGCNA Publication | Manual
• psRNAtarget Publication | Website
• ShinyGO Publication | Website