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
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
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