Hello,
I am a little confused with the interpretation of SAM flags
From http://ppotato.wordpress.com/2010/08...-paired-reads/
...
0×0010 16 strand of the query (0 for forward; 1 for reverse strand)
--
0×0040 64 the read is the first read in a pair
0×0080 128 the read is the second read in a pair
What is the difference? Shouldn't forward correspond to first read in a pair and reverse correspond to second read in a pair?
I have a bam file with paired-unmapped reads- I am trying to extract the reads and mates into separate files. How would I use the SAM flag to figure this out please?
I have read related stuff about this on the forum, but I am new to this, and cannot quite parse the exact information I need from it. Thank you so much!
I am a little confused with the interpretation of SAM flags
From http://ppotato.wordpress.com/2010/08...-paired-reads/
...
0×0010 16 strand of the query (0 for forward; 1 for reverse strand)
--
0×0040 64 the read is the first read in a pair
0×0080 128 the read is the second read in a pair
What is the difference? Shouldn't forward correspond to first read in a pair and reverse correspond to second read in a pair?
I have a bam file with paired-unmapped reads- I am trying to extract the reads and mates into separate files. How would I use the SAM flag to figure this out please?
I have read related stuff about this on the forum, but I am new to this, and cannot quite parse the exact information I need from it. Thank you so much!
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