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Old 03-29-2011, 09:58 PM   #1
nadir
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Location: Pune, India

Join Date: Mar 2011
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Default Important fields of SAM file to be considered

Hi all,

A SAM file provides alignment information between a set of reads and a set of reference files. So, when we consider the reads in the SAM file, which other fields besides just the SEQ (the fragment sequence i.e the read) are important from the point of view of the biologists, doctors or researchers?

For example. the quality values (QUAL field), the strand information (obtained from 5th LSB of FLAG field) and the POS seem to be some of the significant fields that could be useful. If you could shed light on the other significant fields (maybe they could even be from the optional fields' section), I would really appreciate it.

Thanks,
Nadir

Last edited by nadir; 03-29-2011 at 10:09 PM.
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