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Hello, please help me find/create small SAM files (e.g. with less than 10 reads) to help me:
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1. better understand the SAM file format, and
2. test bamliquidator (which I helped to develop, but note that my background is in Computer Science not Biology)
For example, to test handling of duplicate reads I manually typed up this example based on the SAM spec (tabs not preserved):
Hello, please help me find/create small SAM files (e.g. With less than 10 reads) to help me: 1. Better understand the SAM file format, and 2. Test bamliquidator (which I helped to develop, but note that my background is in Computer Science not Biology). Acknowledgments The authors of this report would like to thank the numerous people who provided invaluable input on the text and assistance with collecting photographs.Through the incorporation of the smart growth elements defined in 'Smart Growth for Coastal and Waterfront Communities,'we hope to positively impact the future of our coastal and waterfront communities.
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I hope this is correct, but having lots of tiny SAM examples could help me more quickly and confidently understand the SAM spec so I can generate better test cases.
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I am about to create test cases with paired end reads with gaps, and before doing so I hope I might find more tiny SAM examples and/or better resources given my background.
I have found this link useful for manually creating SAM files: http://genome.ucsc.edu/goldenPath/help/bam.html
Thanks