A question about masking before alignment

[解铎(Xieduo)]

Dear Sir/Madam,

 

I have watched the webpage(http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto) in UCSC wiki about the masking before alignment, and it reads “MASKING: Both genomes have to be repeatmasked and masked Tandem Repeat Finder (trf) first (thanks to Hiram for pointing this out)”.

And then I have two questions about the masking:

1.    Why just use the repeat annotation of repeatmasker and trf ?How to determin the criteria that what kind of repeat annotations should we use?  Can I use the repeat annotation consist of repeatmodeler,repeatmasker and repeatmodeler?

2.    Which masking method should we use? Hardmask or softmask? Will softmask cause the false negative problem?

 

Thank you very much!

 

 

Best！
Duo

 

[Hiram Clawson]

Good Morning Duo:

You can use any masking you would like to use. The key is, if you do
not have enough masking, the alignments will be extremely large outputs
and very difficult to push through the process. For example, you
could add window masker masking to the repeat masker and TRF to get
even more masking. You do not want to use hard masking, that eliminates
sequence that would be useful. Soft masking allows lastz to start
an alignment in sequence that is not masked, and then extend the
alignment into a masked region. Hard masking would prevent this
type of alignment.

--Hiram

[Brian Lee]

Dear Duo,

Thank you for using the UCSC Genome Browser and your question about masking before alignment.

We use RepeatMasker and TRF because they work well for human and other vertebrates. NCBI uses WindowMasker. You may want to experiment with different tools to figure out which tool works best for your genomes and analysis needs. In general, less masking means more sensitivity, but can also lead to a huge amount of output for repetitive or low-complexity regions.

For your second question, we use softmasked sequences. Using lastz does not begin an alignment in a softmasked sequence, but it can extend an alignment through softmasked sequence if doing so increases the score of the alignment.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

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[解铎(Xieduo)]

Dear Brian and Hiram,

Thank you very much  for your quick reply and it is very helpful!

Best!

Duo

---

发件人: Brian Lee <bria...@soe.ucsc.edu>
发送时间: 2018年5月16日 0:19:23
收件人: Hiram Clawson
抄送: 解铎(Xieduo); gen...@soe.ucsc.edu
主题: Re: [genome] A question about masking before alignment