man cosmetics

README.md

@@ -32,7 +32,7 @@
 
 *   If installing manually, you will need Python3 (3.8 or higher), [gffutils](https://pythonhosted.org/gffutils/installation.html), [pysam](https://pysam.readthedocs.io/en/latest/index.html), [pybedtools](https://daler.github.io/pybedtools/), [biopython](https://biopython.org/) and some other common Python libraries to be installed. See `requirements.txt` for details. You will also need to have [minimap2](https://github.com/lh3/minimap2) and [samtools](http://www.htslib.org/download/) to be in your `$PATH` variable.
 
-*   Verify installation
+*   Verify your installation by running:
 
         isoquant.py --test
 
@@ -45,11 +45,10 @@
 
     For example, using the toy data provided within this repository,
 
-        mkdir toy_data_fastq_assembly
         ./isoquant.py --reference tests/toy_data/MAPT.Mouse.reference.fasta \
         --genedb tests/toy_data/MAPT.Mouse.genedb.gtf \
         --fastq tests/toy_data/MAPT.Mouse.ONT.simulated.fastq \
-        --data_type assembly -o toy_data_fastq_assembly
+        --data_type nanopore -o toy_data_out
 
 
 * To run IsoQuant on aligned reads (make sure your BAM is sorted and indexed) use the following command:
@@ -61,19 +60,18 @@
 
     For example, using the toy data provided within this repository,
 
-        mkdir toy_data_bam_assembly
         ./isoquant.py --reference tests/toy_data/MAPT.Mouse.reference.fasta \
         --genedb tests/toy_data/MAPT.Mouse.genedb.gtf \
         --fastq tests/toy_data/MAPT.Mouse.ONT.simulated.fastq \
-        --data_type assembly -o toy_data_bam_assembly
+        --data_type nanopore -o toy_data_out
 
 * If using official annotations containing `gene` and `transcript` features use `--complete_genedb` to save time.
 
 * Using reference annotation is optional since version 3.0, you may preform de novo transcript discovery without providing `--genedb` option':
 
         isoquant.py --reference /PATH/TO/reference_genome.fasta \
         --fastq /PATH/TO/sample1.fastq.gz /PATH/TO/sample2.fastq.gz \
-        --data_type (assembly|pacbio_ccs|nanopore) -o OUTPUT_FOLDER
+        --data_type (assembly|pacbio|nanopore) -o OUTPUT_FOLDER
 
 * If multiple files are provided, IsoQuant will create a single output annotation and a single set of gene/transcript expression tables.