Bioinformatics Recipe Cookbook
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Use SAM flags to make scientific discoveries. (work in progress)

This recipe follows a publication titled Genome-wide antisense transcription drives mRNA processing in bacteria published in PNAS, 2011.

The data was published under the Bioproject: PRJNA80817

The recipe is meant to demonstrate the use of alignments and samtools to find evidence of antisense transcription in Staphylococcus aureus.

In addition, the recipe is meant to train you on identifying the properties of sequencing data from the alignments.

The recipe is not quite ready yet, but already contains useful information.

Lecture

coming soon

Recipe Code
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Integer values
                        [size]
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
                    
Float values
                        [cutoff]
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
                    
Text box
                    [sra]
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
                    
Dropdown menu
                    [color]
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
                    
Check box
                    [validate]
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
                    
Upload Field
                    [file]
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
                    
Pick Data
                    [data]
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
                    
Radio Buttons
                    [species]
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
                    
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