Hi all,
I'm using published data that includes all reads from an experiment and am not familiar with the SAM/BAM output. I'm having trouble interpreting the bitwise flag and MAPQ values to extract uniquely mapping reads and understand appropriate cut-offs.
The SAM FAQ says to use samtools view -q 1 in order to extract "unique" reads; to which value does q refer? MAPQ?
I want to replicate the number of acceptable reads in the publications using their criteria: "The best alignment was kept only in cases in which the second-best alignment had at least three more mismatches." What sort of q value (MAPQ) would this be?
In all, I just want to be confident that I can filter out all unique reads.
Thanks for any help!
Further info: the dataset is single end bisulfite treated and only has 10 bitwise flags:
0
4
16
512
516
528
1024
1040
1536
1552
I'm using published data that includes all reads from an experiment and am not familiar with the SAM/BAM output. I'm having trouble interpreting the bitwise flag and MAPQ values to extract uniquely mapping reads and understand appropriate cut-offs.
The SAM FAQ says to use samtools view -q 1 in order to extract "unique" reads; to which value does q refer? MAPQ?
I want to replicate the number of acceptable reads in the publications using their criteria: "The best alignment was kept only in cases in which the second-best alignment had at least three more mismatches." What sort of q value (MAPQ) would this be?
In all, I just want to be confident that I can filter out all unique reads.
Thanks for any help!
Further info: the dataset is single end bisulfite treated and only has 10 bitwise flags:
0
4
16
512
516
528
1024
1040
1536
1552
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