kallisto_tsv_merging.sh

#!/bin/bash

# Merging kallisto output TSVs

SPECIES=$1

errs=`awk '{print $1}' SAMPLES`
names=`awk '{print $2}' SAMPLES`

a=( $errs )
b=( $names )

for i in `seq 0 5`; do echo ${b[$i]} > ${b[$i]}.tmp ; awk '{if (NR>1) print $4}' ${a[$i]}_kallisto_out/abundance.tsv >> ${b[$i]}.tmp; done
paste *tmp > All_counts.txt

for i in `seq 0 5`; do echo ${b[$i]} > ${b[$i]}.tmp ; awk '{if (NR>1) print $5}' ${a[$i]}_kallisto_out/abundance.tsv >> ${b[$i]}.tmp; done
paste *tmp > All_tpm.txt

paste gencode.${SPECIES}.3col_annotation.txt All_tpm.txt > exp_tpm.txt
paste gencode.${SPECIES}.3col_annotation.txt All_counts.txt > exp_counts.txt