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- SAM (Sequence Alignment Map) format specification (pdf)
- sam/bam tools
- samtools - sam/bam conversion, flag filtering, bam sort/index
- Picard - sam/bam utilities that are read-group aware
- Translate SAM file flags - type in a decimal number to see which flags are set
- SAMstat - produces detailed graphical statistics for sam/bam files.
- BEDTools - region overlap, merge, coverage & much more, w/bed, bam, vcf, gff support
- BEDTools manual on readthedocs.org
UCSC Genome Browser
- intro
- Visualize mapped data at UCSC genome browser on this wiki
- Main UCSC Genome Browser web site
- Beta Test browser site - most up-to-date datasets and features; can be buggy
- File formats - BED format especially is widely used
- Table browser - Browse and download data in different formats
- ENCODE data downloads at UCSC - useful for getting data to work with
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