How to set the length when make a mask fasta file for Glycine_max.Glycine_max_v2.0.dna.fa

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termius

• July 17, 2020 08:45

Hello, I am trying to make a mask fasta file for Glycine_max.Glycine_max_v2.0.dna.fa,but i don't know that How to set the length,can you help me.

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  Genevieve Brandt (she/her)

  • July 17, 2020 18:14

  Hi termius, here is the documentation index: http://software.broadinstitute.org/software/genomestrip/index.html

  Bob Handsaker may also be able to help you with this. 

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  Bob Handsaker

  • July 17, 2020 21:11

  The length (kmer size) to use for the mask depends on the length of the sequencing reads. For typical modern WGS reads (151bp or larger) we typically use 101bp. It is good to use something a little shorter than the actual read length. There is not much difference (at least in human) using something larger than 101bp.

   

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