Usage and parameters

First example: small prokaryotes genome

Let us consider this command line:

sequana_rnaseq --input-directory ../data --aligner bowtie2 --genome-directory  leptospira 

An analysis could be as simple as that. You need to tell the pipeline where to find the fastq.gz file using --input-directory option. Then, you should decide upon the aligner to be used (here bowtie2). Since RNAseq aligns reads on a reference and uses annotation for the feature count, you should indicate the path where to find the genome and its annotation. It should be a directory (here leptospira). The pipeline expects to find leptospira.fa and leptospira.gff file (or .gbk).

All other options have default values.

• strandness is guessed but you can force the pipeline to use your choice.

You may need to edit the config file to set parameters of feature counts so as to decide on counting reads on exon or genes.

Note that we check whether the reference genome has already been indexed. If not, run the sequana_rnaseq pipeline using "--do-indexing " option.

Eukaryotes

The only difference with the previous command is to set the aligner to star.

If a GFF has no rRNA and the rRNA are present in a different FastA file, you can set the --rRNA-feature to nothing ("") and later on, you can edit the config file to indicate where the dedicated FastA file can be found.

sequana_rnaseq --input-directory data/ --genome-directory hg38 --aligner  star --force --rRNA-feature ""