BWA MapQ field

[yaten2020]

Hi all,
I am using BWA for my illumina/single-end/ChIP-seq reads (36 bases). In MAPQ filed I can see values as 0, 4, 5, 25, 37 etc. Can anyone tell me which reads I should go ahead for peak calling ?

In other words, what should be the threshold for MAPPING QUALITY in a typical ChP-seq experiment ?

regards
YK

[nilshomer]

hi all
i am using BWA for my illumina single-end chip-seq reads (36 bases). in MAPQ filed i can see values as 0, 4, 5, 25, 37 etc. can anyone help me which reads i should go ahead for peak calling ? i read in SAM maunal about this field being phred scaled. does it mean i need to filter my file for good MAPQ values and discard everything else. if yes .... then which ones i should keep?

regards
yk

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