Update README.md

bulkRNAseq/README.md

+**Bulk RNAseq** data analysis workflow includes the following steps:
 
-
+1. Quality control by [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+2. Trimming of bad quality reads with [TrimGalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+3. Alignment with [STAR](https://github.com/alexdobin/STAR)
+    <details><summary>Running command</summary>
+            "STAR " +
+            "--runThreadN {threads} " +
+            "--genomeDir {input.genome} " +
+            "--readFilesIn {params.trim_seq} " +
+            "--outSAMstrandField intronMotif " +
+            "--outFileNamePrefix {params.aln_seq_prefix} " +
+            "--outSAMtype BAM SortedByCoordinate " +
+            "--outSAMmultNmax 1 " +
+            "--outFilterMismatchNmax 10 " +
+            "--outReadsUnmapped Fastx " +
+            "--readFilesCommand zcat "
+    </details>
+4. Gene expression quantification with [FeatureCounts](https://academic.oup.com/bioinformatics/article/30/7/923/232889)
+    <details><summary>Running command</summary>
+            "featureCounts " +
+            "-a {input.annot} " +
+            "-o {output.fcount} " +
+            "-g gene_name " +
+            "-p -B -C " +
+            "-s {params.strand} " +
+            "--minOverlap 10 " +
+            "-T {threads} " +
+            "{input.bams} "
+    </details>