Hi,
I am working on genomics data (ChIP-Seq, SR100) and for this I used bwa mem (no "XT:A:U" tag) for aligning the fastq files.
After, I am finding peaks with MACS.
It is necessary to use a filter on the minimum mapping quality (MAPQ)...
What is the best way to remove reads that map to multiple locations?
What cutoff value do you use about MAPQ?
There are very different answers depending on the forums...
I think it is only necessary to remove zeros but I don't find a consensus or recommendations for good practice...
thank you !!
Emeric
I am working on genomics data (ChIP-Seq, SR100) and for this I used bwa mem (no "XT:A:U" tag) for aligning the fastq files.
After, I am finding peaks with MACS.
It is necessary to use a filter on the minimum mapping quality (MAPQ)...
What is the best way to remove reads that map to multiple locations?
What cutoff value do you use about MAPQ?
There are very different answers depending on the forums...
I think it is only necessary to remove zeros but I don't find a consensus or recommendations for good practice...
thank you !!
Emeric
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