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Old 03-28-2016, 07:30 PM   #3
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Join Date: Mar 2016
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Originally Posted by Richard Finney View Post
3rd read flag value 401 has not primary alignment bit.

2nd read has "SA" tag:
SA is : Other canonical alignments in a chimeric alignment, formatted as a semicolon-delimited list: ( rname , pos , strand , CIGAR , mapQ , NM [[...]+. Each element in the list represents a part of the chimeric alignment. Conventionally, at a supplementary line, the [...] element points to the primary line.

it's pointing to 3rd read via the location.

So, looks like your software suppors reads that have parts that maps to different locations.
Thank you for your reply!

I read your reply carefully but there is some difficulty for me to understand.

Could you explain the three reads more easy to understand? or how can I solve the warnings "Could not find pair for HWI-ST430:177:2:1:4979:15503#0".

Thank you very much!

Last edited by Alphabets; 03-28-2016 at 07:51 PM.
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