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