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Week 3 : Filetypes and Browser
Introduction to Bioinformatics (LF:DSIB01)

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Encoding Genomic Information for Bioinformatics Use
•Location Based Formats (.bed)
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•Count/Coverage Based Formats (.bedgraph .wig)
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•Feature Based Formats (.gtf)
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•Sequence Based Formats (.fasta .fastq)
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•Multiple Alignment Files
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•Alignment Based Formats (.sam)
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BED (Browser Extensible Data) file format
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-Tab Delimited Text File
-Number of columns consistent per line
-No Empty fields (some can have “.” as N/A)
BED 3 columns : chrom, chromStart, chromEnd
BED 6 columns : BED3 + name, score, strand
BED 12 columns : BED6 + thickStart, thickEnd, itemRGB, blockCount, blockSizes, blockStarts
https://genome.ucsc.edu/FAQ/FAQformat.html#format1

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BED 3 columns : chrom, chromStart, chromEnd
BED 6 columns : BED3 + name, score, strand
BED 12 columns : BED6 + thickStart, thickEnd, itemRGB, blockCount, blockSizes, blockStarts

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BED pros and cons
•Generic
•Human Readable
•Useful for simple genomic loci
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•Awkward handling of splice events
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•Not useful for variable scores
•Must repeat BED3 info every line
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bedGraph
•Used to display continuous data
•Header “browser” + Header “track” + Sorted BED lines (chr, start, stop, score)
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wiggle file (.wig)
•Comes in two flavors: variablestep vs fixed step
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Wig pros and cons
•Compact
•Wide variety of values
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•Difficult for human readability
•Difficult to add/subtract lines
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General transfer format (.gtf)
•Also commonly known as .gff (general feature format)
•1. seqname (chr)
•2. source (program generating seq)
•3. feature (what is it? “CDS”, “exon”, “enhancer” etc)
•4. start (position)
•5. end (inclusive)
•6. score (can be any float. Ideal: between 1-1000 for UCSC browser)
•7. strand (“+”, “-”, “.”)
•8. frame (for exons, frame is between 0-2 representing open reading frame, else “.”)
•9. group; list of attributes (gene_id, transcript_id etc)
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Fasta & Fastq
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Fastq Quality Scores
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Multiple Alignment File
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Sequence Alignment Map (.sam)
•https://www.samformat.info/
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Sequence Alignment Map (.sam)
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.bam format
(Binary SAM)

Adobe Systems
Encoding Genomic Information for Bioinformatics Use
•Location Based Formats (.bed)
•
•Count/Coverage Based Formats (.bedgraph .wig)
•
•Feature Based Formats (.gtf)
•
•Sequence Based Formats (.fasta .fastq)
•
•Multiple Alignment Files
•
•Alignment Based Formats (.sam)
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