# Galaxy NGS Illumina SE Mapping
This tutorial shows how to perform basic QC on Illumina data, such as basic quality statistics, quality score boxplots, trimming and masking.
### Single-End Mapping of Illumina Data
**1. Load fastq file and annotate the uploaded data**
* On the Tool Panel, click on Get Data → Upload File.
* This tools allows you to upload a data from a file, url or a textbox.
* Select *Galaxy\_GM12878\_trimmed.fastq* as input file.
* Select "fastqsanger" as file format.
* Select "hg18" as genome.
* Click the "Execute" button.
**2. Map to reference genome (hg18) using Bowtie**
* On the Tool Panel, click on NGS Toolbox Beta → NGS Mapping → Map with Bowtie for Illmina.
* This tools allows you to run the aligner Bowtie. The output is a SAM files with all the read alignments.
* Select *hg canonical* as reference genome.
* Leave other settings as default.
* Click the "Execute" button.
**3. Filter SAM file on bitwise flag values**
* On the Tool Panel, click on NGS Toolbox Beta → NGS SAMtools → Filter SAM on bitwise flag values.
* This tools
* Select data 2 as input dataset.
* Add new flag with type set to "the read is unmapped" and the value set to "No".
* Add new flag with type set to "read strand" and the value set to "Yes".
* Click the "Execute" button.
* With these parameters, the resulting output consists of those reads that are properly mapped and are on the reverse strand.
**4. Find how many reads map to each chromosome**
* On the Tool Panel, click on Join, Subtract and Group → Group →
* This tools
* Select data 2 (bowtie output) as input dataset.
* Group by column 3 (reference name, i.e. chromosome name)
* Add new operation: count on column 1 .
* Click the "Execute" button.
* With these parameters, the resulting output consists of those reads that are properly mapped and are on the reverse strand.
* Edit the attributes of this module by clicking on the eye icon: rename as "read distribution by chromosome".
**5. Find the most represented chromosome**
* On the Tool Panel, click on Filter and Sort → Sort data →
* This tools
* Select the column representing the key to sort
* Select "Numerical sort" in "descending order" as options.
* Click the "Execute" button.
* With these parameters, the results show that chr19 is the most represented chromosome.
**6. Convert SAM to BAM**
* On the Tool Panel, click on NGS Toolbox Beta→ NGS Samtools \&rarr SAM to BAM converter.
* This tools converts SAM-formatted files into BAM-formatted files.
* Select the SAM file to convert.
* Click the "Execute" button.
**7. Compute general statistics via Flagstat operation**
* On the Tool Panel, click on NGS Toolbox Beta→ NGS Samtools \&rarr flagstat.
* This tools provides a simple summary based on BAM-format.
* Select data 6 (BAM file) as input.
