wrap_sample.sh

```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

##run align_and_estimate_abundance.pl (Trinity framework) for several samples
### run for leafs
cd  /home/annag/RNA_seq_roots/MERGE/processed_sa/unmapped_sa/Leaf_done

for k in $(ls *.fastq | rev | cut -c 10- | rev | uniq)
	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 ${k}_r1.fq --right ${k}_r2.fq --est_method RSEM --aln_method bowtie --trinity_mode --thread_count 6 --output_dir /home/annag/T_PP_NB_R_7/SA_clean_Trinity/Abundance/Abundance_by_sample/${k}_RSEM/
	done


### bowtie_PE_separate_then_join:


TRINITY_HOME/util/bowtie_PE_separate_then_join.pl --seqType fq \
              --left left.fq --right right.fq \
              --target Trinity.fasta --aligner bowtie \
              -- -p 4 --all --best --st

rata -m 300  # following -- are params that get tacked onto the bowtie command.
```