pipeline for RNA-seq of soil README
Adriana L. Romero-Olivares' protocol for processing RNAseq data of soil
This pipeline is divided in 8 sections. Each section has a filename and a step
Section 1
File name: 1_clean_trim_QC
Step: Cleaning-trimming-fastQC of raw reads
Section 2
File name: 2_sortmeRNA
Step: Preparing files for assembly with Trinity
Section 3
File name: 3_assembly_de_novo
Step: Assembly with Trinity
Section 4
File name: 4_align_bowtie2
Step: Alignment of reads with bowtie2
Section 5
File name: 5_quant_express
Step: Quantification of reads
Section 6
File name: 6_diff_expresion
Step: Differential expression analysis
Section 7
File name: 7_annotate_metatranscriptome
Step: Annotate meta-transcriptome
Section 8
File name: 8_create_annotated_metatranscriptome
Step: Create annotated meta-transcriptome