gogleva

```sh
#!/bin/bash
##run align_and_estimate_abundance.pl (Trinity framework) for several samples

cd ~/RNA_seq_roots/MERGE/processed_sa/unmapped_sa/Root_done/root_reads_by_sample/

for i in $(ls *.fq | rev | cut -c 7- | rev | uniq)
	# with file names like '4_TGACCA_R1.fq'
	do ~/Assemblers/trinityrnaseq-2.1.0/util/align_and_estimate_abundance.pl --transcripts ~/T_PP_NB_R_7/SA_clean_Trinity/SA_Trinity_clean_assembly/Trinity_clean_run.fasta --seqType fq --left ${i}_R1.fq --right ${i}_R2.fq --est_method RSEM --aln_method bowtie --trinity_mode --thread_count 6 --output_dir /home/annag/T_PP_NB_R_7/SA_clean_Trinity/Abundance/Abundance_by_sample/${i}_RSEM/
	done

gogleva

#################

counts1
counts2
counts3


analyse_DEG <- function(dataset, hpi){
    #0 pre-filter sample table
    sampletable <- SampleTable %>%

gogleva

#! /bin/bash

# This file must be in the same folder as the tarballs.
# Path to the folder should be short (< 60 characters) #to do warings

### EDIT 2 LINES BELOW #########################################################
# SS_dep SS_out will be created in the directory with tarballs. Please replace 
# "SS_dep" with full path to the directory, e.g "/home/tools/SS_dep" and
# "SS_out" - accordingly.  
export SSDEP="SS_dep"