Kallisto code

Here is Kallisto code in Linux operating system for the Sample 1 of the project:

 #!/bin/bash -l
#SBATCH -A g2016025
#SBATCH -t 2:00:00
#SBATCH -p node -n 8
#SBATCH -o my_job_out

## Step:1  Indexing transcriptome file -coding and non -coding DNA- for pseudoalignment.
#This line generates the Transcriptome-De Bruijn graph using hashing of k-mers (default value:31 #base length).

kallisto index -i transcripts.idx Homo_sapiens.GRCh38.cdna.all.fa.gz Homo_sapiens.GRCh38.ncrna.fa.gz  transcripts_all.idx

## Step 2: Run main kallisto command for paired-end RNA seq data on sample 1 with default #parameters (except number of bootstraps = 100 bootstraps -to be used at a later stage for quantifying #technical noise)

# Sample 1
kallisto quant -i sequences/transcript_reference/transcripts_all.idx -o kallisto.outputS1 -b 100 S1/S01_FR_line1.fq.gz S1/S01_RR_line1.fq.gz S1/S01_FR_line2.fq.gz S1/S01_RR_line2.fq.gz S1/S01_FR_line3.fq.gz S1/S01_RR_line3.fq.gz S1/S01_FR_line4.fq.gz S1/S01_RR_line4.fq.gz S1/S01_FR_line5.fq.gz S1/S01_RR_line5.fq.gz

## The output consists of three different files :
#abundances.tsv (text file with abundance estimates)
#abundances.h5 (hdf5 file with abundance estimates along with bootstrap estimates, run #info,transcript length information length)
#run_info.json(json file with details abou the run)