Question: Contents Of A Sam File
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gravatar for Benjamin Osei-agyeman
5.1 years ago by
Benjamin Osei-agyeman80 wrote:
Hi What are the contents of a SAM file after Bowtie has been run? Does it contain all reads or only those reads mapped to the genome? Thanks Benjy
alignment bowtie • 1.3k views
ADD COMMENTlink modified 5.1 years ago by Jeremy Goecks2.2k • written 5.1 years ago by Benjamin Osei-agyeman80
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gravatar for Jeremy Goecks
5.1 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
All reads are in the SAM file; you can filter to remove unmapped reads as needed. J.
ADD COMMENTlink written 5.1 years ago by Jeremy Goecks2.2k
Thanks a lot, If i want to extract the unmapped reads from the SAM file after bowtie has run do I have to use Samtools or can this be done straightaway using galaxy? What command should I use? Thanks Benjy
ADD REPLYlink written 5.1 years ago by Benjamin Osei-agyeman80
Hi Benjy, To extract unmapped reads from a SAM file in Galaxy, you can use 'Filter SAM' ('NGS: SAM Tools' -> 'Filter SAM'). Add a 'flag' and use the 'The read is unmapped' type, then set the state for this flag to 'Yes'. This should return a SAM file with your unmapped reads. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Thu, Nov 7, 2013 at 1:22 PM, Benjamin Osei-agyeman <
ADD REPLYlink written 5.1 years ago by Mohammad Heydarian100
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