namlab-mapper

Convenience script in Nextflow to download and map multiple RNA sequences from SRA to the same reference at once using kallisto and combine all the abundance quantifications into one table.

Prerequisites

rnaseq-mapper will try to load the following modules: sratoolkit, kallisto, R, fastqc. If your system doesn't use modules, make sure the execs are available in your PATH. I'm currently working on a Singularity container that packages all the required software (see singularity_container.def).

Usage

1. Set up nextflow (if not installed already):

curl -s https://get.nextflow.io | bash

2. Create a file nextflow.config by using the example_nextflow.config from this directory as a template and adapting it to your use case.
3. Create an input file with the sequences you want to map in the format of example_input.csv and make sure it is referred to in your config file.
4. Run the pipeline:

./nextflow run NAMlab/rnaseq-mapper

Output

You will get out a TSV file with the combined kallisto outputs for all your sequences like this one:

target_id	length	SRR1805735_eff_length	SRR1805735_est_counts	SRR1805735_tpm	SRR1805737_eff_length	SRR1805737_est_counts	SRR1805737_tpm	SRR6512869_eff_length	SRR6512869_est_counts	SRR6512869_tpm
Solyc00g005280.1.1	411	252.224	0	0	241.253	0	0	212	0	0
Solyc00g005285.2.1	216	68.6464	0	0	63.7937	0	0	31.5146	0	0
Solyc00g006483.2.1	390	231.296	0	0	220.691	0	0	191	0	0
Solyc00g006487.2.1	276	120.525	0	0	114.108	0	0	77.4659	2	22.2662
Solyc00g006560.2.1	1317	1158	0	0	1145.76	0	0	1118	0	0
Solyc00g006890.2.1	300	143.123	0	0	135.795	0	0	101.044	0	0
Solyc00g006900.2.1	576	416.999	0	0	404.931	0	0	377	0	0
Solyc00g007225.2.1	1275	1116	0	0	1103.76	0	0	1076	0	0
Solyc00g007330.1.1	516	356.999	0	0	345.082	0	0	317	0	0

You will also get FastQC reports for each of the downloaded sequences.